SNP6 Copy number analysis (GISTIC2)
Colon Adenocarcinoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
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/C1154G63
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 450 tumor samples used in this analysis: 23 significant arm-level results, 25 significant focal amplifications, and 43 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 - 25 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
20q11.21 2.4957e-42 1.9164e-24 chr20:26197900-30582729 26
13q12.13 2.6527e-26 1.1783e-19 chr13:27521847-27533641 0 [USP12]
8q24.21 5.4842e-20 2.1411e-19 chr8:128389850-128754688 3
17q12 1.6704e-14 8.4935e-14 chr17:37837542-38021723 6
20q12 4.0491e-38 2.2067e-12 chr20:35722356-40360023 52
11p15.5 1.2336e-09 1.2336e-09 chr11:2141587-2244703 5
8p11.23 2.2685e-12 1.3401e-09 chr8:38170522-38237581 1
12p13.33 3.3506e-08 3.3506e-08 chr12:2055585-4699385 21
20q13.12 1.8067e-13 5.3313e-08 chr20:42493784-43357898 15
13q22.1 4.6993e-12 1.0409e-07 chr13:73599695-74055302 3
5q22.3 5.7934e-07 5.7934e-07 chr5:114756122-114759166 0 [FEM1C]
8p11.21 2.5458e-10 2.3355e-05 chr8:41614677-42365372 12
20p11.21 5.2226e-17 0.00063594 chr20:25355954-25483163 3
6p21.1 0.0044563 0.0044563 chr6:40092319-44407505 94
19q13.11 0.0088227 0.0088227 chr19:32351550-33019554 3
8q12.1 0.0001178 0.012623 chr8:42932479-70211670 109
5p13.2 0.031213 0.031213 chr5:27059148-50133343 90
19p13.2 0.03438 0.03438 chr19:7300056-7398264 0 [INSR]
16p11.2 0.031213 0.071815 chr16:30641164-30720446 3
20p12.1 0.067255 0.086764 chr20:14111361-17415432 9
2q33.1 0.12071 0.12071 chr2:199627908-199644614 0 [PLCL1]
17q24.1 0.0041221 0.12551 chr17:57733799-81195210 355
17p11.2 0.058872 0.1366 chr17:21124724-21305391 4
7p21.2 0.17501 0.17501 chr7:1-63128930 391
16q12.1 0.094806 0.23326 chr16:51079810-53017796 7
Genes in Wide Peak

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

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

Genes
XKR7
LINC00028
DEFB122
SNORA40|ENSG00000212134.1
RNA5SP480
BCL2L1
FOXS1
ID1
TPX2
REM1
HM13
PDRG1
COX4I2
MYLK2
DEFB118
DUSP15
TTLL9
DEFB115
DEFB116
DEFB119
DEFB121
DEFB123
DEFB124
FRG1B
MIR663A
MIR3193
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q24.21.

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

Genes
MYC
POU5F1B
CASC8
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q12.

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

Genes
ERBB2
IKZF3
MIR4728
GRB7
MIEN1
PGAP3
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q12.

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

Genes
TOP1
MAFB
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
BPI
GHRH
LBP
NNAT
PLCG1
RBL1
RPN2
SRC
TGM2
TTI1
BLCAP
ZHX3
PPP1R16B
CTNNBL1
RALGAPB
RPRD1B
DHX35
MANBAL
LPIN3
ACTR5
FAM83D
CHD6
KIAA1755
EMILIN3
VSTM2L
SNHG11
SLC32A1
MROH8
ADIG
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p15.5.

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

Genes
MIR483
IGF2
INS
TH
MIR4686
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.23.

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

Genes
WHSC1L1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p13.33.

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

Genes
CCND2
C12orf5
FKBP4
CBX3P4
CACNA1C
FGF6
FOXM1
TEAD4
TULP3
FGF23
DYRK4
RAD51AP1
TSPAN9
ITFG2
PRMT8
PARP11
C12orf4
RHNO1
NRIP2
EFCAB4B
DCP1B
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.12.

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

Genes
MIR3646
R3HDML
FITM2
RN7SL443P
ADA
HNF4A
WISP2
SERINC3
PKIG
OSER1
JPH2
GDAP1L1
TTPAL
TOX2
C20orf62
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q22.1.

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

Genes
LINC00393
RNY1P8
KLF5
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.21.

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

Genes
snoU13|ENSG00000238714.1
SNORD112|ENSG00000238966.1
RN7SL149P
ANK1
IKBKB
PLAT
POLB
SLC20A2
VDAC3
KAT6A
AP3M2
DKK4
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20p11.21.

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

Genes
GINS1
NINL
ABHD12
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.1.

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

Genes
CCND3
TFEB
MIR4642
TCTE1
TMEM151B
RSPH9
SCARNA15|ENSG00000252218.1
RN7SL403P
MEA1
snoU13|ENSG00000238611.1
U3|ENSG00000221252.1
GUCA1B
SNORA8|ENSG00000206977.1
TOMM6
MIR4641
RNA5SP207
TREML3P
NFYA
APOBEC2
LINC00951
TDRG1
BYSL
CDC5L
SLC29A1
GUCA1A
HSP90AB1
MDFI
NFKBIE
PEX6
PGC
POLH
PPP2R5D
PTK7
PRPH2
SRF
TBCC
VEGFA
NCR2
MED20
POLR1C
MAD2L1BP
CUL7
DNPH1
CNPY3
FRS3
SLC22A7
CAPN11
CUL9
UBR2
GLTSCR1L
ZNF318
YIPF3
USP49
GNMT
PRICKLE4
MRPL2
TREM2
TREM1
GTPBP2
MRPS18A
MRPS10
TMEM63B
TRERF1
LRFN2
AARS2
XPO5
MRPL14
DLK2
TREML2
TTBK1
RRP36
ABCC10
KLC4
TJAP1
FOXP4
KLHDC3
TAF8
PTCRA
SPATS1
C6orf223
LRRC73
ADCY10P1
OARD1
TSPO2
UNC5CL
TREML4
RPL7L1
TREML1
SLC35B2
CRIP3
C6orf226
TMEM151B
C6orf132
MIR4647
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.11.

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

Genes
RNA5SP472
ZNF507
DPY19L3
Genes in Wide Peak

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

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

Genes
PLAG1
TCEA1
CHCHD7
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
ASPH
CRH
CYP7A1
FNTA
LYN
MCM4
MOS
MYBL1
OPRK1
PENK
PRKDC
RAB2A
RP1
SDCBP
SNAI2
TTPA
NSMAF
RGS20
GGH
CYP7B1
MTFR1
ST18
TOX
RB1CC1
LYPLA1
ARFGEF1
COPS5
RRS1
SPIDR
SGK3
BHLHE22
ATP6V1H
SNTG1
IMPAD1
ARMC1
CHD7
C8orf44
CPA6
SOX17
EFCAB1
CSPP1
VCPIP1
SGK196
TRIM55
DNAJC5B
FAM110B
TGS1
PCMTD1
C8orf34
TMEM68
ADHFE1
UBXN2B
PXDNL
HGSNAT
MCMDC2
CLVS1
SDR16C5
YTHDF3
C8orf46
PPP1R42
FAM150A
C8orf22
SNHG6
TCF24
MIR4470
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p13.2.

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

Genes
LIFR
HCN1
RN7SL383P
FGF10
CCL28
ANXA2R
SNORD72
RPL37
SNORA57|ENSG00000212567.1
SNORA63|ENSG00000199552.1
LINC00604
LINC00603
WDR70
RN7SL37P
RNA5SP181
LMBRD2
U3|ENSG00000201368.1
BRIX1
C1QTNF3
MIR579
snoU13|ENSG00000238864.1
RN7SKP207
SNORA18|ENSG00000252601.1
C6
C7
C9
CDH6
CDH9
DAB2
FYB
GDNF
GHR
HMGCS1
IL7R
NPR3
OXCT1
PRKAA1
PRLR
PTGER4
RAD1
SEPP1
SKP2
SLC1A3
TARS
ZNF131
OSMR
NUP155
PAIP1
MRPS30
SUB1
PDZD2
NNT
TTC33
AMACR
NIPBL
RAI14
FBXO4
DROSHA
SLC45A2
RXFP3
ZFR
MTMR12
C5orf22
GOLPH3
C5orf28
AGXT2
C5orf42
PARP8
SPEF2
ADAMTS12
CARD6
EMB
MROH2B
EGFLAM
NADK2
UGT3A1
CAPSL
DNAJC21
TTC23L
UGT3A2
NIM1
RANBP3L
RICTOR
C5orf51
PLCXD3
C5orf34
MIR580
CCDC152
MIR4279
MIR3650
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16p11.2.

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

Genes
SRCAP
FBRS
PRR14
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20p12.1.

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

Genes
U3|ENSG00000212165.1
RNA5SP475
RN7SL864P
PCSK2
SNRPB2
FLRT3
KIF16B
OTOR
MACROD2
Genes in Wide Peak

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

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

Genes
BRIP1
CD79B
CLTC
DDX5
PRKAR1A
ASPSCR1
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
AANAT
ACOX1
ACTG1
BIRC5
APOH
ARHGDIA
CA4
CACNG1
CD7
CDK3
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
MAFG
MAP3K3
NPTX1
P4HB
PDE6G
PRKCA
PRPSAP1
PSMC5
PYCR1
RAC3
RFNG
RPL38
MRPL12
RPS6KB1
SCN4A
SEC14L1
SECTM1
SRSF2
SGSH
SMARCD2
SUMO2
SOX9
SRP68
TBCD
TBX2
TIMP2
TK1
AXIN2
CBX4
DNAH17
RGS9
GALR2
SPHK1
SOCS3
SLC16A6
SLC16A5
SLC16A3
SYNGR2
HGS
CYTH1
SLC9A3R1
COG1
RECQL5
PGS1
TBX4
AATK
KIAA0195
EIF4A3
MRC2
HELZ
MED13
ALYREF
DCAF7
ABCA10
ABCA9
ABCA8
BAIAP2
ATP5H
APPBP2
ST6GALNAC2
GNA13
SEPT9
CD300C
POLG2
CD300A
TMC6
DDX42
AZI1
GGA3
JMJD6
EXOC7
ABCA6
ABCA5
KCTD2
WBP2
CDC42EP4
FSCN2
NOL11
TANC2
NAT9
PITPNC1
NARF
CACNG5
CACNG4
SAP30BP
NT5C
CDR2L
MRPS7
RNFT1
HN1
TUBD1
DCXR
TACO1
AMZ2
ANAPC11
SIRT7
PTRH2
SDK2
BCAS3
TMEM104
C17orf80
CCDC40
WIPI1
NPLOC4
ST6GALNAC1
TEX2
WDR45B
CCDC47
MIF4GD
INTS2
CASKIN2
RPTOR
USP36
RNF213
TNRC6C
SLC25A19
UBE2O
HEATR6
FN3K
DNAI2
MRPL38
CARD14
MFSD11
C17orf62
ARMC7
CHMP6
RHBDF2
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
SLC38A10
USH1G
CD300LB
KIF19
C17orf64
TBC1D16
AFMID
MGAT5B
ENTHD2
B3GNTL1
RBFOX3
CD300LF
C17orf77
EFCAB3
NOTUM
TMC8
MARCH10
CEP112
STRA13
LRRC45
SLC39A11
AMZ2P1
TRIM65
UNC13D
MYADML2
NPB
FADS6
HID1
TSEN54
UBALD2
TMEM235
CCDC57
HEXDC
C17orf58
MILR1
SLC26A11
ENDOV
C17orf89
TMEM105
METRNL
RAB37
METTL2A
ENPP7
OXLD1
CCDC137
ARL16
CD300E
NACA2
OTOP3
FAM195B
GPR142
ZACN
LRRC37A3
C17orf82
BTBD17
TEX19
MIR21
MXRA7
CPSF4L
SMIM5
MIR633
SMIM6
TEN1
C17orf99
MIR4316
MIR338
MIR3186
MIR3678
MIR3615
MIR4739
MIR4737
MIR4738
MIR4740
MIR4524B
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17p11.2.

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

Genes
RN7SL426P
KCNJ12
MAP2K3
C17orf103
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p21.2.

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

Genes
HOXA13
EGFR
ETV1
HNRNPA2B1
HOXA9
HOXA11
PMS2
IKZF1
CARD11
JAZF1
RN7SL855P
ZNF733P
RN7SL816P
snoU13|ENSG00000238673.1
PHKG1
SNORA15|ENSG00000207168.1
SNORA22|ENSG00000206603.1
RN7SL64P
ZNF713
MRPS17
SNORA73|ENSG00000252054.1
VSTM2A
snoU13|ENSG00000238354.1
RN7SKP218
snoU13|ENSG00000238506.1
SNORA31|ENSG00000253028.1
RN7SL292P
SNORA4|ENSG00000201133.1
C7orf72
VWC2
LINC00525
EPS15P1
SEPT7P2
SNORA5B
SNORA5C
SNORA5A
SNHG15
NUDCD3
RNA5SP230
MIR4649
LINC00957
RASA4CP
POLR2J4
MIR3943
HECW1
PSMA2
INHBA
MPLKIP
RN7SL496P
LINC00265
SNORA20|ENSG00000206947.1
RN7SL83P
TRGV1
TRGV2
TRGV3
TRGV4
TRGV5
TRGV8
TRGV9
TRGV10
TRGV11
TRGJP1
TRGJP
TRGJ1
TRGC1
TRGJP2
TRGJ2
TRGC2
SNORA51|ENSG00000200113.1
snoU13|ENSG00000238772.1
MIR1200
PP13004
SEPT7
DPY19L2P1
MIR548N
SNORA31|ENSG00000251802.1
RN7SL132P
RNA5SP229
snoU13|ENSG00000252706.1
RN7SL505P
RP9P
SNORA31|ENSG00000251999.1
AQP1
CRHR2
MIR550A1
snoU13|ENSG00000238906.1
TRIL
RN7SL365P
EVX1
HOTTIP
HOTAIRM1
U3|ENSG00000202233.1
CYCS
snoU13|ENSG00000239098.1
RNA5SP228
snoU13|ENSG00000238849.1
SNORD65|ENSG00000212264.1
MALSU1
SNORD93
RNA5SP227
MIR1183
RN7SL542P
SP8
SNORD56|ENSG00000200753.1
MIR3146
RN7SKP266
SNORA63|ENSG00000199473.1
ISPD
RN7SKP228
SNORA64|ENSG00000199470.1
TMEM106B
U3|ENSG00000212422.1
RPA3
PMS2CL
GRID2IP
FLJ20306
RN7SL851P
SNORA42|ENSG00000207217.1
RN7SL556P
ZNF815P
MIR589
snoU13|ENSG00000238394.1
ZNF890P
RNF216P1
AP5Z1
snoU13|ENSG00000238781.1
RN7SKP130
snoU13|ENSG00000238857.1
MIR4648
GRIFIN
MIR4655
ELFN1
UNCX
MIR339
COX19
FAM20C
ACTB
ADCY1
ADCYAP1R1
AEBP1
AHR
AMPH
AOAH
AQP1
BLVRA
CAMK2B
CCT6A
CHN2
DGKB
DDC
DFNA5
GARS
GBAS
GCK
GHRHR
GLI3
GNA12
GPER
GRB10
HOXA1
HOXA2
HOXA3
HOXA4
HOXA5
HOXA6
HOXA7
HOXA10
HUS1
ICA1
IGFBP1
IGFBP3
IL6
ITGB8
LFNG
MEOX2
NUDT1
NDUFA4
NPY
OGDH
PDE1C
PDGFA
PGAM2
POLD2
PPIA
PRKAR1B
PSMA2
PSPH
PURB
RAC1
RALA
RP9
SFRP4
FSCN1
SP4
TWIST1
UPP1
ZNF12
AIMP2
MAFK
MAD1L1
CDK13
EIF3B
DNAH11
TAX1BP1
SKAP2
TBRG4
STK17A
CYTH3
CREB5
NFE2L3
PHF14
HDAC9
RAPGEF5
SCRN1
KIAA0087
ELMO1
ARL4A
RAMP3
NOD1
GPNMB
AGR2
IGF2BP3
YKT6
PPP1R17
KDELR2
ADAP1
ZPBP
NUPL2
HIBADH
INMT
POU6F2
FKBP9
CBX3
AVL9
NACAD
SNX13
COBL
IQCE
DPY19L1
SUN1
KIAA0895
SEC61G
LSM5
SUMF2
SOSTDC1
KBTBD2
OSBPL3
WIPI2
INTS1
VPS41
TSPAN13
EIF2AK1
BBS9
POLM
BZW2
DBNL
NPC1L1
SNX8
SNX10
TRA2A
FTSJ2
NXPH1
CHCHD2
NT5C3A
NME8
MRPS17
GET4
UBE2D4
CCZ1
MPP6
ANLN
MIOS
RNF216
CPVL
TOMM7
DDX56
EPDR1
ZNF853
CYP2W1
HEATR2
FKBP14
ZDHHC4
CHST12
CDCA7L
URGCP
RADIL
COA1
LANCL2
KLHL7
STK31
PAPOLB
C1GALT1
YAE1D1
ANKMY2
TBX20
RBAK
MYL7
NEUROD6
FIGNL1
MYO1G
NPVF
HERPUD2
TNS3
MRPS24
MRPL32
GGCT
C7orf25
C7orf26
MICALL2
C7orf10
FBXL18
C7orf69
TTYH3
EEPD1
VOPP1
CCM2
ZMIZ2
STARD3NL
USP42
FAM188B
PSMG3
C7orf50
TNRC18
FAM126A
PLEKHA8
FAM220A
SCIN
ZFAND2A
CCDC126
ZNF479
H2AFV
GLCCI1
GPR146
C7orf57
C7orf31
ABCA13
AMZ1
AGR3
PKD1L1
BMPER
TMEM184A
VWDE
PRPS1L1
TWISTNB
BRAT1
SDK1
FOXK1
MMD2
DAGLB
CCZ1B
THSD7A
TMED4
C7orf41
PRR15
FERD3L
SLC29A4
RSPH10B
CCDC129
ZNRF2
TMEM196
STEAP1B
SUN3
POM121L12
C7orf71
SPDYE1
COL28A1
ABCB5
FAM221A
FAM183B
SEPT14
MACC1
GPR141
FKBP9L
NPSR1
NUPR1L
AGMO
C7orf65
MIR148A
ZNF716
MIR196B
WIPF3
OCM
MIR550A2
RSPH10B2
ANKRD61
MIR3147
MIR3683
LRRC72
MIR550A3
MIR4657
MIR4656
Genes in Wide Peak

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

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

Genes
CASC16
LINC00919
RN7SKP142
HNRNPA1P48
SALL1
TOX3
C16orf97

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 - 43 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
16p13.3 1.3469e-119 1.3469e-119 chr16:5144019-7780235 2
4q22.1 9.6128e-45 1.9091e-42 chr4:91271445-93240505 1
20p12.1 2.8682e-42 2.8682e-42 chr20:14301156-15274325 2
6q26 6.8395e-42 6.8395e-42 chr6:161693099-163153207 1
16q23.1 2.9884e-32 2.9884e-32 chr16:78098006-79031486 1
3p14.2 1.7965e-32 2.7056e-31 chr3:59701447-61547330 3
1p33 1.1285e-34 3.9913e-31 chr1:49615826-50514967 1
5q12.1 2.345e-25 5.295e-23 chr5:58998410-59780946 2
18q21.2 3.6174e-25 1.9171e-22 chr18:48472083-48650073 3
3q26.31 3.4636e-22 3.3039e-22 chr3:174345545-175760559 3
1p36.11 5.1775e-24 7.1549e-20 chr1:26527443-27650365 29
6p25.3 2.3691e-18 2.2904e-18 chr6:1608837-2624052 2
4q35.1 1.5728e-18 4.5748e-15 chr4:179280062-186507186 41
10q21.1 1.8319e-16 8.8871e-15 chr10:53057593-53461574 2
8p22 1.1244e-13 6.3347e-10 chr8:15092726-16722285 3
10q23.31 1.889e-14 1.5788e-09 chr10:89313008-90034038 7
5q22.2 1.3512e-18 8.7923e-07 chr5:109202065-115142292 30
18q12.2 9.6097e-15 1.092e-06 chr18:36593175-39537209 2
7q31.1 2.19e-05 2.173e-05 chr7:110746146-111366370 1
17p12 5.6471e-05 5.7037e-05 chr17:11060240-12456081 7
19p13.3 8.189e-05 7.8334e-05 chr19:1033227-1907478 35
21q11.2 0.00010569 0.00011083 chr21:1-26470028 39
5q21.1 8.6152e-14 0.00013928 chr5:90456284-108085742 52
15q22.33 2.1613e-05 0.00014412 chr15:67067796-67494822 1
8p23.3 7.6085e-10 0.00045967 chr8:1-4985851 15
22q13.32 0.00051594 0.00051594 chr22:48668761-51304566 42
15q11.2 6.36e-09 0.0019379 chr15:1-28001323 58
15q15.2 1.3554e-09 0.0032197 chr15:37383162-44050111 103
15q21.1 1.4304e-08 0.016773 chr15:44953604-45299932 4
18p11.31 0.018377 0.018475 chr18:3277692-5145388 6
9p21.3 0.038913 0.038732 chr9:21410163-23690570 11
17q24.3 0.042149 0.041313 chr17:68173089-70642789 2
10q25.2 1.2165e-06 0.0604 chr10:100989718-135534747 286
14q31.1 0.059696 0.0604 chr14:58447798-107349540 504
8q11.1 0.060833 0.062499 chr8:42883855-47750537 6
12p13.2 0.077561 0.077029 chr12:9360276-16500867 104
3p26.2 0.0068394 0.085721 chr3:1-21472074 142
1p13.1 0.00033661 0.11466 chr1:58878852-149898950 494
10p15.3 0.13181 0.13367 chr10:1-5407870 36
1q43 0.15615 0.15615 chr1:228127228-240178106 122
4p16.2 0.15498 0.15615 chr4:1-10442121 143
2p21 0.15884 0.15986 chr2:40835958-45880121 28
2q22.1 0.18641 0.18679 chr2:121098198-168815541 195
13q14.13 0.25536 0.24755 chr13:34674944-71590578 207
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16p13.3.

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

Genes
SNORA40|ENSG00000252138.1
RBFOX1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q22.1.

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

Genes
RN7SKP248
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20p12.1.

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

Genes
RNA5SP475
FLRT3
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q26.

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

Genes
PARK2
Genes in Wide Peak

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

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

Genes
PIH1
Genes in Wide Peak

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

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

Genes
FHIT
U3|ENSG00000212211.1
NPCDR1
Genes in Wide Peak

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

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

Genes
snoU13|ENSG00000239144.1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q12.1.

Table S29.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
FKSG52
MIR582
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q21.2.

Table S30.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SL695P
SMAD4
ELAC1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q26.31.

Table S31.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
snoU13|ENSG00000271842.1
MIR4789
RN7SKP40
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.11.

Table S32.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ARID1A
GPN2
ZDHHC18
RN7SL165P
RN7SL501P
snoU13|ENSG00000238316.1
RN7SL679P
MIR1976
HMGN2
RN7SL490P
AIM1L
SH3BGRL3
CD52
SFN
RPS6KA1
SLC9A1
NR0B2
NUDC
WDTC1
PIGV
GPATCH3
CEP85
LIN28A
DHDDS
UBXN11
FAM46B
C1orf172
ZNF683
TRNP1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p25.3.

Table S33.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
FOXC1
GMDS
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.1.

Table S34.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PDLIM3
UFSP2
SNORD79
RN7SL28P
snoU13|ENSG00000239116.1
snoU13|ENSG00000238596.1
snoU13|ENSG00000238319.1
U3|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173
SLC25A4
CASP3
DCTD
ACSL1
ING2
IRF2
CLDN22
CDKN2AIP
TENM3
LRP2BP
STOX2
KIAA1430
TRAPPC11
MLF1IP
WWC2
SNX25
ENPP6
RWDD4
CCDC111
CCDC110
ANKRD37
HELT
C4orf47
CLDN24
MIR1305
MIR3945
MIR4455
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q21.1.

Table S35.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
MIR605
CSTF2T
Genes in Wide Peak

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

Table S36.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SL474P
MSR1
TUSC3
Genes in Wide Peak

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

Table S37.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PTEN
SNORD74|ENSG00000200891.1
RN7SL78P
CFL1P1
PAPSS2
ATAD1
KLLN
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q22.2.

Table S38.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
APC
RN7SKP89
RNU4ATAC13P
ZRSR1
SRP19
FLJ11235
SNORA13
RN7SKP57
CAMK4
SNORA51|ENSG00000207177.1
MIR548F3
TMEM232
KCNN2
MCC
PGGT1B
REEP5
NREP
TMED7
TRIM36
FEM1C
EPB41L4A
YTHDC2
TSSK1B
TSLP
SLC25A46
STARD4
WDR36
CCDC112
DCP2
TICAM2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q12.2.

Table S39.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
LINC00669
RN7SKP182
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q31.1.

Table S40.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
snoU13|ENSG00000238922.1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p12.

Table S41.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
MAP2K4
MIR744
RPL21P122
RN7SL601P
DNAH9
ZNF18
SHISA6
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p13.3.

Table S42.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
STK11
TCF3
MIR1909
ONECUT3
UQCR11
RN7SL477P
NDUFS7
C19orf24
POLR2E
ATP5D
CIRBP
EFNA2
GAMT
GPX4
RPS15
APC2
ABCA7
UQCR11
SBNO2
HMHA1
DAZAP1
MBD3
PCSK4
REXO1
ABHD17A
KLF16
MUM1
MIDN
REEP6
PLK5
C19orf25
ATP8B3
C19orf26
ADAMTSL5
MEX3D
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q11.2.

Table S43.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SL609P
LINC00308
LINC00317
LINC00320
RN7SKP147
RN7SL163P
SNORD74|ENSG00000201025.1
snoU13|ENSG00000238591.1
RNA5SP488
ANKRD20A11P
CYP4F29P
ANKRD30BP2
BAGE2
SNORA70|ENSG00000252199.1
RN7SL52P
TEKT4P2
MIR3648
CXADR
NCAM2
TMPRSS15
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
C21orf91
SAMSN1
CHODL
LIPI
ABCC13
POTED
LINC00478
MIRLET7C
MIR125B2
MIR99A
MIR548X
MIR3687
C21orf37
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q21.1.

Table S44.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SKP122
RN7SL782P
SNORA31|ENSG00000252337.1
RNA5SP189
RN7SL255P
LINC00491
LINC00492
RN7SKP68
RNA5SP188
RN7SL802P
MIR548P
RN7SKP62
GPR150
LUCAT1
CAST
CHD1
EFNA5
GLRX
LNPEP
PAM
PCSK1
NR2F1
ST8SIA4
TTC37
RHOBTB3
ELL2
PPIP5K2
ERAP1
GIN1
RIOK2
ARRDC3
ERAP2
FBXL17
MCTP1
NUDT12
SPATA9
FAM172A
ANKRD32
C5orf30
SLCO6A1
POU5F2
ARSK
FAM81B
LIX1
C5orf27
KIAA0825
RGMB
RFESD
FAM174A
SLCO4C1
MIR583
MIR2277
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q22.33.

Table S45.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
SMAD3
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.3.

Table S46.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SL872P
RNA5SP251
RPL23AP53
OR4F21
CLN8
MYOM2
DLGAP2
ARHGEF10
KBTBD11
FBXO25
CSMD1
TDRP
ERICH1
ZNF596
MIR596
Genes in Wide Peak

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

Table S47.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ARSA
RN7SL500P
DENND6B
TTLL8
ALG12
RN7SKP252
ACR
CHKB
CPT1B
TYMP
MAPK11
MAPK12
SBF1
PPP6R2
ZBED4
SCO2
RABL2B
MLC1
MAPK8IP2
PLXNB2
BRD1
FAM19A5
NCAPH2
MOV10L1
MIOX
PANX2
CRELD2
ADM2
TRABD
HDAC10
SHANK3
TUBGCP6
LMF2
KLHDC7B
C22orf34
IL17REL
PIM3
ODF3B
SYCE3
MIR3201
MIR3667
MIR4535
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q11.2.

Table S48.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RNA5SP391
LINC00929
SNORA48|ENSG00000212604.1
MIR4715
RNA5SP390
ATP10A
SNORD109B
SNORD115|ENSG00000212428.1
SNORD109A
SNORD108
SNORD64|ENSG00000270704.2
SNHG14
SNURF
snoU13|ENSG00000238615.1
PWRN1
PWRN2
MAGEL2
RN7SL536P
GOLGA8S
RN7SL106P
HERC2P2
RN7SL495P
WHAMMP3
RN7SL545P
GOLGA8DP
MIR1268A
OR4N4
snoU13|ENSG00000238960.1
DKFZP547L112
RN7SL400P
CT60
NBEAP1
RN7SL759P
GOLGA6L6
snoU13|ENSG00000239083.1
CHEK2P2
RN7SL584P
GABRA5
GABRB3
GABRG3
NDN
SNRPN
UBE3A
MKRN3
CYFIP1
NPAP1
NIPA2
TUBGCP5
NIPA1
GOLGA6L2
HERC2P3
GOLGA6L1
GOLGA8I
GOLGA8EP
OR4M2
POTEB2
MIR4508
POTEB
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q15.2.

Table S49.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
BUB1B
CATSPER2P1
snoU13|ENSG00000238494.1
snoU13|ENSG00000238535.1
RN7SL487P
CCNDBP1
snoU13|ENSG00000239025.1
MIR627
MIR4310
RNA5SP393
MIR626
RN7SL497P
RN7SL376P
snoU13|ENSG00000238559.1
LINC00594
RNA5SP392
LINC00984
snoU13|ENSG00000238564.1
THBS1
FAM98B
CAPN3
CKMT1B
EPB42
GANC
GCHFR
ITPKA
IVD
LTK
MAP1A
PLCB2
RAD51
SPINT1
SRP14
TP53BP1
TYRO3
SNAP23
TGM5
PPIP5K1
LCMT2
RASGRP1
GPR176
CHP1
OIP5
BAHD1
MAPKBP1
RTF1
MGA
VPS39
TMEM87A
RPAP1
RPUSD2
TUBGCP4
EHD4
NDUFAF1
NUSAP1
SPTBN5
DLL4
INO80
PPP1R14D
HAUS2
RMDN3
DNAJC17
PAK6
CASC5
STARD9
VPS18
ZNF106
CHAC1
TMEM62
ZFYVE19
DISP2
C15orf57
KNSTRN
BMF
CHST14
TGM7
CATSPER2
PLA2G4E
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
SPRED1
ADAL
EXD1
FSIP1
RHOV
UBR1
PLA2G4F
LRRC57
PLA2G4D
C15orf52
C15orf53
C15orf54
EIF2AK4
CKMT1A
C15orf62
C15orf56
PHGR1
ANKRD63
JMJD7
PLA2G4B
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q21.1.

Table S50.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
B2M
TRIM69
C15orf43
PATL2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18p11.31.

Table S51.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
snoU13|ENSG00000238790.1
snoU13|ENSG00000238445.1
RN7SL39P
snoU13|ENSG00000238863.1
TGIF1
DLGAP1
Genes in Wide Peak

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

Table S52.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
DMRTA1
RN7SL151P
SNORD39|ENSG00000264379.1
MIR31HG
CDKN2A
CDKN2B
IFNA1
MTAP
C9orf53
IFNE
MIR31
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q24.3.

Table S53.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
LINC00511
SOX9
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q25.2.

Table S54.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
FGFR2
TLX1
NFKB2
SUFU
MIR3944
TUBGCP2
C10orf91
BNIP3
PPP2R2D
LINC00959
MIR4297
MGMT
NPS
SNORD60|ENSG00000199321.1
RNA5SP328
MIR4296
METTL10
GPR26
MIR3941
RN7SKP167
RN7SL846P
TIAL1
MIR4681
RN7SL749P
FAM45A
SNORA19|ENSG00000222588.1
SNORA19|ENSG00000207468.1
U3|ENSG00000251836.1
LINC00867
EMX2OS
PDZD8
ENO4
snoU13|ENSG00000238577.1
RN7SL384P
VWA2
NHLRC2
SNORA17|ENSG00000212589.1
MIR4295
GUCY2GP
MIR548E
RNA5SP327
RN7SKP288
RN7SL686P
snoU13|ENSG00000239125.1
SMNDC1
RN7SL450P
U4|ENSG00000272160.1
RN7SKP278
RNA5SP326
RNA5SP325
snoU13|ENSG00000238620.1
ITPRIP
MIR609
MIR936
RN7SL524P
OBFC1
C10ORF32
SFXN2
RN7SL21P
SNORD112|ENSG00000253068.1
FGF8
snoU13|ENSG00000239091.1
SNORD112|ENSG00000252844.1
LBX1
HUG1
KAZALD1
MIR608
HIF1AN
NDUFB8
LINC00263
BLOC1S2
SNORA12|ENSG00000212464.1
ERLIN1
snoU13|ENSG00000238472.1
COX15
ENTPD7
snoU13|ENSG00000238588.1
ACADSB
ADAM8
ADD3
ADRA2A
ADRB1
ARL3
CASP7
CHUK
ABCC2
COL17A1
CPN1
CTBP2
CYP2E1
CYP17A1
DMBT1
DOCK1
DUSP5
ECHS1
EMX2
GFRA1
GOT1
PRLHR
GRK5
HABP2
HMX2
INPP5A
ABLIM1
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
HTRA1
PSD
PTPRE
RGS10
SCD
FBXW4
SLC18A2
TAF5
TCF7L2
TECTB
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
EIF3A
GBF1
LDB1
BTRC
PKD2L1
INA
SMC3
NEURL
BUB3
NOLC1
GSTO1
BAG3
SH3PXD2A
FAM53B
SLK
DCLRE1A
ACTR1A
NPM3
GLRX3
DPYSL4
TACC2
MGEA5
PRDX3
VAX1
ATE1
SEC23IP
RAB11FIP2
INPP5F
NT5C2
PDCD11
SORCS3
PPRC1
FAM175B
DNMBP
DPCD
SEC31B
ATRNL1
C10orf137
CNNM1
PDCD4
VENTX
POLL
KCNIP2
CUZD1
CALY
CALHM2
CUTC
CHST15
ACSL5
ZRANB1
TTC40
NSMCE4A
CNNM2
WBP1L
C10orf118
CWF19L1
WDR11
FAM178A
DHX32
TDRD1
BCCIP
C10orf2
AS3MT
GPAM
KIAA1598
FAM160B1
SEMA4G
PLEKHA1
FAM204A
LHPP
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
TMEM180
MCMBP
C10orf95
PLEKHS1
PDZD7
C10orf88
WDR96
LRRC27
TRIM8
SFXN3
SLC25A28
ELOVL3
PCGF6
GPR123
LZTS2
MRPL43
AFAP1L2
USMG5
KNDC1
MTG1
BBIP1
FANK1
SYCE1
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
MMP21
C10orf32
GSTO2
SFR1
CALHM3
CLRN3
PNLIPRP3
SFXN4
CPXM2
TRUB1
VTI1A
C10orf82
CACUL1
CCDC147
PWWP2B
PPAPDC1A
PAOX
FAM24B
EBF3
CALHM1
CASC2
TCERG1L
HSPA12A
FUOM
JAKMIP3
STK32C
RBM20
KCNK18
NANOS1
HMX3
CCDC172
ARMS2
TEX36
C10orf120
FOXI2
C10orf85
FRG2B
SPRN
MIR146B
MIR202
FAM196A
TLX1NB
MIR1307
MIR2110
MIR378C
MIR3663
MIR4680
MIR4682
MIR4484
LINC00601
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q31.1.

Table S55.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
AKT1
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
TCL6
BCL11B
RNA5SP389
LINC00221
LINC00226
ADAM6
KIAA0125
IGHJ1
IGHJ2
IGHJ3
IGHJ4
IGHJ5
IGHJ6
IGHM
IGHD
IGHG3
IGHG1
IGHA1
IGHG2
IGHG4
IGHE
IGHA2
CRIP1
C14orf79
LINC00638
ZBTB42
C14orf144
RN7SL634P
LINC00637
SNORD51|ENSG00000202275.1
APOPT1
SNORA28
LINC00605
LINC00677
snoU13|ENSG00000238853.1
RN7SL546P
snoU13|ENSG00000239061.1
RN7SL472P
LINC00524
U3|ENSG00000206761.1
MEG9
MIR369
MIR377
MIR485
MIR134
MIR382
MIR381HG
MIR376A1
MIR376C
MIR380
MIR299
MIR379
SNORD113|ENSG00000222185.1
SNORD112|ENSG00000252009.1
SNORD113|ENSG00000222095.1
SNORD113|ENSG00000201710.1
SNORD113|ENSG00000201036.1
SNORD113|ENSG00000201500.1
SNORD113|ENSG00000200150.1
SNORD112|ENSG00000251918.1
SNORD112|ENSG00000252144.1
SNORD112|ENSG00000251949.1
SNORD112|ENSG00000252873.1
SNORD112|ENSG00000251769.1
MEG8
MIR433
MEG3
RN7SKP92
RN7SL523P
YY1
DEGS2
MIR342
CCNK
U6|ENSG00000272439.1
RN7SL714P
RN7SL710P
LINC00618
RN7SKP108
snoU13|ENSG00000238776.1
DKFZP434O1614
C14orf132
LINC00617
GLRX5
SCARNA13
SNHG10
MIR4506
SLC24A4
NDUFB1
U3|ENSG00000200042.1
RN7SL506P
SNORA11B
LINC00642
RN7SKP255
RN7SKP107
KCNK10
GPR65
LINC00911
RNU3P3
RNU6ATAC28P
snoU13|ENSG00000238978.1
SNORA79|ENSG00000221303.1
NRXN3
RNA5SP388
RN7SL587P
SNORA46|ENSG00000212371.1
FKSG61
SAMD15
RN7SL137P
TMED8
SNORA32|ENSG00000201384.1
RN7SL356P
RN7SKP17
RN7SL747P
TGFB3
C14orf1
RNA5SP387
RNU4ATAC14P
SNORA7|ENSG00000222604.1
ISCA2
MIR4709
RN7SL530P
LIN52
ENTPD5
snoU13|ENSG00000238330.1
ACOT4
C14orf169
RN7SL586P
snoU13|ENSG00000238972.1
RN7SL683P
SNORD56B
RN7SL77P
ADAM20P1
SYNJ2BP
ADAM21P1
SNORA11|ENSG00000221060.1
SLC10A1
CCDC177|ENSG00000267909.1
CCDC177|ENSG00000255994.1
ERH
RN7SL224P
RN7SL108P
RN7SL706P
RN7SL213P
U3|ENSG00000252792.1
RN7SL369P
ATP6V1D
MIR4706
FNTB
ZBTB25
U3|ENSG00000200693.1
WDR89
SCARNA20|ENSG00000252800.1
RN7SL540P
PPP2R5E
GPHB5
LINC00644
LINC00643
SNORD112|ENSG00000252380.1
SIX1
U3|ENSG00000253014.1
SIX6
MIR5586
JKAMP
GPR135
ACTR10
RN7SL598P
C14orf37
SERPINA3
ACTN1
ACYP1
ARG2
BDKRB1
BDKRB2
ZFP36L1
CALM1
SERPINA6
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
EML1
ESR2
ESRRB
FOS
FUT8
GALC
GPX2
GSTZ1
GTF2A1
BRF1
HIF1A
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LTBP2
MARK3
MAX
ATXN3
MAP3K9
ALDH6A1
MNAT1
MTHFD1
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPM1A
PPP2R5C
PRKCH
LGMN
PSEN1
PSMA3
PSMC1
ABCD4
RAD51B
MOK
ARID4A
RTN1
SEL1L
SRSF5
SLC8A3
SNAPC1
SPTB
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
DPF3
GPR68
NUMB
ADAM21
ADAM20
DLK1
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
KIAA0586
AREL1
TECPR2
MED6
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
VASH1
ZBTB1
SNW1
PCNX
DAAM1
TTLL5
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
TMEM251
PLEK2
TIMM9
MLH3
KCNH5
GPR132
POMT2
COQ6
FCF1
RDH11
SERPINA10
COX16
DACT1
EVL
GSKIP
CINP
DHRS7
ASB2
SIX4
ZFYVE1
CPSF2
CDCA4
NRDE2
ATG2B
UBR7
EXD2
VRTN
SLC39A9
FLVCR2
GPATCH2L
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
YLPM1
KCNK13
DDX24
ADCK1
TMEM63C
RHOJ
GALNT16
PLEKHH1
TRMT5
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
VIPAS39
SMOC1
MOAP1
IRF2BPL
MPP5
INF2
PCNXL4
OTUB2
ZFYVE21
WDR25
LINC00341
ZC2HC1C
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
CCDC176
TMEM121
SGPP1
AMN
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
SETD3
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
CHURC1
ELMSAN1
NEK9
EXOC3L4
WDR20
IFT43
L3HYPDH
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
PLD4
ADSSL1
NOXRED1
JDP2
TTC8
TC2N
SLC25A29
RDH12
GSC
SERPINA12
PRIMA1
PPP1R36
SLC38A6
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
SYNE3
TMEM30B
EML5
NUDT14
LINC00521
SERPINA11
PROX2
ZDHHC22
C14orf178
C14orf177
SLC25A47
LINC00523
CEP170B
C14orf80
C14orf39
CCDC85C
SERPINA9
VSX2
LRRC9
COX8C
ASPG
RAB15
TOMM20L
SERPINA13P
C14orf64
RTL1
TMEM179
HEATR4
PLEKHD1
C14orf180
MIR127
MIR136
MIR154
MIR203
LINC00238
CCDC88C
MIR323A
MIR337
MIR345
MIR370
MIR381
MIR431
MIR323B
MIR409
MIR412
MIR410
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
SYNDIG1L
RD3L
TEX22
MIR539
MIR544A
MIR487B
MIR411
MIR625
MIR654
MIR655
MIR656
CCDC175
MIR758
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
DIO3OS
MIR1260A
MIR1197
MIR548H1
MIR1193
MIR4309
MIR3173
MIR4505
MIR4708
MIR151B
MIR4710
MIR2392
MIR5694
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8q11.1.

Table S56.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
RN7SKP41
U3|ENSG00000201329.1
POTEA
FNTA
SGK196
HGSNAT
Genes in Wide Peak

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

Table S57.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ETV6
ERP27
ART4
C12orf60
RN7SKP134
PLBD1
RPL30P11
RN7SL676P
RN7SL46P
RN7SKP162
GRIN2B
RNA5SP353
HTR7P1
SNORD88
GPRC5A
MIR613
DUSP16
LOH12CR2
TAS2R30
TAS2R64P
TAS2R20
TAS2R14
PRH2
TAS2R8
MAGOHB
EIF2S3L
RN7SKP161
KLRF2
CLEC2B
CLEC2D
KLRB1
SNORA75|ENSG00000212432.1
SNORA75|ENSG00000212440.1
LINC00987
A2MP1
ARHGDIB
CD69
CDKN1B
CREBL2
EMP1
EPS8
GPR19
GUCY2C
KLRC1
KLRC2
KLRC3
KLRD1
LRP6
MGP
OLR1
PDE6H
PRB1
PRB3
PRB4
PRH1
PTPRO
KLRC4
YBX3
KLRAP1
STRAP
PRR4
KLRK1
GABARAPL1
TAS2R9
TAS2R7
TAS2R13
TAS2R10
HEBP1
DERA
DDX47
CLEC1B
CLEC1A
KLRF1
WBP11
MANSC1
STYK1
GPRC5D
ATF7IP
H2AFJ
KIAA1467
CLEC7A
BCL2L14
APOLD1
GSG1
RERG
LOH12CR1
TMEM52B
HIST4H4
CLEC12A
CLECL1
TAS2R43
TAS2R31
TAS2R46
TAS2R19
TAS2R50
CLEC9A
C12orf36
TAS2R42
CLEC2A
CLEC12B
SMCO3
PRB2
MIR614
SLC15A5
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p26.2.

Table S58.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
VHL
FANCD2
PPARG
RAF1
XPC
SRGAP3
RNY4P22
MIR3135A
U7|ENSG00000271841.1
LINC00690
DPH3
RN7SL4P
MIR3134
RN7SL110P
MIR4270
snoU13|ENSG00000238891.1
COL6A4P1
NR2C2
GRIP2
RNA5SP124
LSM3
FGD5P1
WNT7A
LINC00620
SNORA7A
snoU13|ENSG00000239140.1
C3orf83
RNA5SP123
SYN2
RN7SL147P
SLC6A11
LINC00606
MIR885
GHRLOS
LINC00852
snoU13|ENSG00000238345.1
snoU13|ENSG00000238642.1
CIDECP
EMC3
LHFPL4
SNORA43|ENSG00000199815.1
LINC00312
RNU4ATAC17P
RN7SL553P
snoU13|ENSG00000239126.1
EGOT
SNORA43|ENSG00000253049.1
RN7SKP144
RN7SL120P
ATP2B2
BTD
CAV3
DAZL
FBLN2
GRM7
HRH1
IL5RA
IRAK2
ITPR1
OGG1
OXTR
RAB5A
RPL32
SATB1
SEC13
SETMAR
SLC6A1
SLC6A6
TIMP4
BRPF1
COLQ
CAMK1
BHLHE40
KAT2B
SH3BP5
VGLL4
EDEM1
TBC1D5
TATDN2
IQSEC1
ARPC4
TADA3
ATG7
CHL1
CAND2
RFTN1
NUP210
PLCL2
ANKRD28
CAPN7
MKRN2
THUMPD3
HACL1
TTLL3
CNTN6
LMCD1
SSUH2
TRNT1
CRBN
CCDC174
GHRL
ARL8B
SETD5
TMEM40
BRK1
RAD18
LRRN1
CIDEC
ZFYVE20
MTMR14
MRPS25
CRELD1
TMEM43
HDAC11
TSEN2
C3orf20
JAGN1
IL17RC
EAF1
OXNAD1
FANCD2OS
GALNT15
KCNH8
CHCHD4
METTL6
TAMM41
IL17RE
SGOL1
PP2D1
EFHB
CPNE9
FGD5
CNTN4
SUMF1
RPUSD3
PRRT3
TPRXL
MIR563
MIR378B
MIR3714
MIR4791
MIR4790
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p13.1.

Table S59.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
BCL9
JAK1
JUN
NOTCH2
NRAS
BCL10
PDE4DIP
TRIM33
RBM15
HIST2H3A
HIST2H2AA3
HIST2H3C
FAM72C
FCGR1C
RNA5SP59
NBPF15
RNA5SP58
NBPF24
RN7SL261P
ACP6
LINC00624
HYDIN2
RNA5SP57
PDZK1P1
RNF115
NUDT17
GNRHR2
NBPF10
SEC22B
RN7SKP88
LINC00623
NBPF8
SRGAP2B
ANKRD20A12P
FCGR1B
HIST2H2BA
LINC00622
snoU13|ENSG00000238679.1
RNA5SP56
WDR3
SNORA40|ENSG00000212266.1
MAN1A2
MIR942
TTF2
RNA5SP55
MIR548AC
ATP1A1OS
U3|ENSG00000221040.1
SNORA42|ENSG00000207502.1
RN7SL420P
RN7SL432P
DENND2C
BCL2L15
LRIG2
snoU13|ENSG00000238975.1
WNT2B
snoU13|ENSG00000238761.1
snoU13|ENSG00000239111.1
ATP5F1
PGCP1
DENND2D
RNA5SP54
CYMP
SNORA25|ENSG00000200536.1
ALX3
RNU6V
GNAI3
KIAA1324
SCARNA2
TMEM167B
TAF13
SPATA42
NBPF5P
SLC25A24P1
RN7SKP285
snoU13|ENSG00000238296.1
SCARNA16|ENSG00000252765.1
DPH5
MIR553
LPPR5
RN7SKP270
RN7SL831P
ALG14
snoU13|ENSG00000238389.1
RN7SL440P
ARHGAP29
GCLM
DNTTIP2
RNA5SP53
DR1
RN7SKP123
RN7SL692P
SNORA51|ENSG00000207022.1
SNORA66|ENSG00000207523.1
SNORA66|ENSG00000251795.1
SNORD21
RN7SL824P
RPAP2
ACTBP12
RN7SL235P
RN7SL653P
BARHL2
U3|ENSG00000199666.1
RN7SKP272
snoU13|ENSG00000239176.1
GBP1P1
GBP6
RN7SL583P
RNA5SP52
RNA5SP51
SNORD81|ENSG00000199934.1
C1orf52
CTBS
SPATA1
RPF1
UOX
SNORA2|ENSG00000199959.1
TTLL7
RN7SKP247
RNA5SP23
RNA5SP22
GIPC2
DNAJB4
RNA5SP21
RN7SL370P
RNA5SP20
ST6GALNAC5
ST6GALNAC3
SNORD45B
SNORD45A
SNORD45C
LRRC53
RNU4ATAC8P
RNA5SP50
RN7SKP19
NEGR1
MIR186
RN7SL242P
PIN1P1
RN7SL538P
MIR1262
RN7SL392P
RNU4ATAC4P
SNORA31|ENSG00000252433.1
MIR3117
RN7SL854P
snoU13|ENSG00000238931.1
LEPROT
MIR4794
RN7SL130P
DLEU2L
RN7SL488P
LINC00466
RNA5SP49
RN7SL180P
RN7SL475P
RN7SL713P
ABCA4
ACADM
ADORA3
AGL
AK4
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CRYZ
CSF1
CTH
CYP2J2
DBT
GADD45A
DPYD
S1PR1
CELSR2
EXTL2
F3
FCGR1A
FMO5
GBP1
GBP2
GBP3
GFI1
GJA5
GJA8
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
HMGCS2
HSD3B1
HSD3B2
IGSF3
CYR61
IL12RB2
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
TACSTD2
MOV10
MSH4
NFIA
NGF
NHLH2
ROR1
OVGP1
PDE4B
PDZK1
PGM1
PRKAB2
PRKACB
PKN2
PSMA5
PTGER3
PTGFR
PTGFRN
ABCD3
RABGGTB
RAP1A
RPE65
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TBX15
TGFBR3
TSHB
USP1
VCAM1
CSDE1
EVI5
CDC7
HIST2H2AC
HIST2H2BE
HIST2H4A
BCAR3
ITGA10
LMO4
CDC14A
RTCA
FPGT
PEX11B
FUBP1
DIRAS3
SLC16A4
SRSF11
CD101
ZRANB2
CHD1L
CLCA3P
CLCA2
HS2ST1
DNAJC6
LPPR4
SV2A
RBM8A
INSL5
PIGK
TSPAN2
INADL
BCAS2
WARS2
CEPT1
PIAS3
VAV3
LAMTOR5
IFI44
POLR3C
TXNIP
AP4B1
PHTF1
AHCYL1
IFI44L
ADAM30
CD160
GLMN
HHLA3
DDX20
CLCA4
MTF2
NTNG1
WDR47
USP33
CLCC1
SLC35D1
LPHN2
KIAA1107
ITGB3BP
SLC35A3
LRRC8B
LPAR3
DDAH1
NBPF14
RWDD3
ZZZ3
SERBP1
PTPN22
PHGDH
AK5
FOXD3
CHIA
ANGPTL3
GPSM2
ALG6
SLC25A24
TMED5
BOLA1
SH3GLB1
HAO2
HOOK1
SNX7
GPR89B
GPR88
TRMT13
L1TD1
RSBN1
ZNHIT6
LEPR
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
RAVER2
FGGY
MCOLN3
SLC22A15
RNPC3
LRRC40
DEPDC1
LRIF1
CTTNBP2NL
FAM212B
GNG12
CCBL2
OLFML3
AMIGO1
ODF2L
LRRC7
CACHD1
MIER1
PTBP2
DNASE2B
ELTD1
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
WDR78
WLS
SIKE1
TRIM45
ANKRD13C
VANGL1
GPR61
TM2D1
REG4
SYDE2
ZNF644
LRRC8C
SGIP1
POLR3GL
PROK1
EFCAB7
PSRC1
ATG4C
STRIP1
DOCK7
ZNF697
NEXN
HENMT1
MYSM1
OMA1
GBP4
GBP5
SSX2IP
OLFM3
WDR63
MAB21L3
SLC44A3
ATXN7L2
C1orf194
ASB17
TYW3
C1orf173
LRRIQ3
LRRC39
C1orf87
LIX1L
DRAM2
PIFO
C1orf162
SYT6
SAMD13
TMEM56
NBPF4
UBE2U
HFE2
ANKRD35
SLC30A7
NBPF12
IL23R
CHIAP2
FNDC7
KANK4
SASS6
PPIAL4A
HFM1
UBL4B
NBPF11
TCTEX1D1
SPAG17
HIPK1
SLC44A5
EPHX4
AKNAD1
MCOLN2
COL24A1
MAGI3
FAM19A3
NBPF16
FAM102B
SYPL2
CYB561D1
ANKRD34A
ZNF326
BTBD8
HIST2H2AB
PPM1J
CCDC18
MYBPHL
FAM73A
GBP7
C1orf146
FAM69A
SLC6A17
C1orf137
NOTCH2NL
FRRS1
C1orf141
NBPF9
MIR197
LHX8
C1orf180
HIST2H2BF
RBMXL1
HIST2H4B
PPIAL4G
PPIAL4D
NBPF6
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
HIST2H2AA4
FAM72D
GPR89C
MIR760
NBPF20
MIR320B1
MIR3671
TNNI3K
MIR378G
MIR4711
MIR137HG
MIR4423
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p15.3.

Table S60.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
AKR1C7P
U8|ENSG00000251909.1
AKR1CL1
U8|ENSG00000239142.1
U8|ENSG00000251740.1
U8|ENSG00000239148.1
U8|ENSG00000238840.1
AKR1C1
LINC00705
LINC00704
LINC00703
LINC00702
LINC00701
LINC00700
ADARB2
MIR5699
RN7SL754P
RNA5SP298
RNA5SP297
TUBB8
AKR1C4
KLF6
AKR1C2
IDI1
PFKP
AKR1C3
PITRM1
ZMYND11
WDR37
DIP2C
LARP4B
GTPBP4
AKR1E2
IDI2
LINC00200
PRR26
Genes in Wide Peak

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

Table S61.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CHRM3
MTRNR2L11
ZP4
SNORA25|ENSG00000252290.1
MIR4428
RN7SKP195
snoU13|ENSG00000252638.1
MIR4753
SNORA14B
RN7SL668P
RNY4P16
LINC00184
U8|ENSG00000212144.1
MIR4671
MIR4427
NTPCR
RN7SL299P
LINC00582
TRAX
RNA5SP80
MIR1182
snoU13|ENSG00000238985.1
RN7SL837P
RNA5SP79
RN7SL467P
RNA5SP78
RN7SKP276
TMEM78
SNORA51|ENSG00000206878.1
RNA5SP18
RNA5S17
RNA5S16
RNA5S15
RNA5S14
RNA5S13
RNA5S12
RNA5S11
RNA5S10
RNA5S9
RNA5S8
RNA5S7
RNA5S6
RNA5S5
RNA5S4
RNA5S3
RNA5S2
RNA5S1
RNA5SP19
BTNL10
RNF187
MIR3620
MIR5008
ACTA1
ACTN2
AGT
ARF1
LYST
GALNT2
GNG4
GUK1
KCNK1
LGALS8
MTR
NID1
RAB4A
RYR2
TARBP1
TBCE
GPR137B
TSNAX
HIST3H3
GNPAT
GGPS1
TOMM20
URB2
SPHAR
CAPN9
COG2
RBM34
ABCB10
TAF5L
DISC1
TRIM17
ARID4B
EGLN1
MAP10
HEATR1
NUP133
ERO1LB
GJC2
SIPA1L2
RHOU
ARV1
C1orf35
TTC13
PGBD5
PCNXL2
TRIM11
SPRTN
OBSCN
MLK4
C1orf198
WNT3A
HIST3H2A
CCSAP
C1orf131
EDARADD
MRPL55
HIST3H2BB
SLC35F3
B3GALNT2
EXOC8
IBA57
IRF2BP2
FAM89A
COA6
TRIM67
C1orf145
C1orf148
MT1HL1
MIR1537
MIR4666A
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p16.2.

Table S62.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
FGFR3
WHSC1
RNA5SP155
MIR3138
RNA5SP154
RNA5SP153
USP17L23
USP17L15
FAM90A26
GPR78
RNA5SP152
MIR95
MIR4274
MIR4798
RN7SKP36
GRPEL1
RN7SKP292
S100P
C4orf50
RN7SKP275
RN7SKP113
FAM86EP
LINC00955
LRPAP1
MSANTD1
RN7SL589P
MIR943
SCARNA22
RN7SL671P
SNORA48|ENSG00000212458.1
TMED11P
RN7SL358P
ZNF721
ABCA11P
MIR571
ZNF141
ZNF732
ZNF876P
ZNF718
ZNF595
ADD1
ADRA2C
ATP5I
CRMP1
CTBP1
DGKQ
DRD5
EVC
GAK
GRK4
HTT
HGFAC
HMX1
IDUA
LETM1
MSX1
MYL5
PDE6B
PPP2R2C
RGS12
RNF4
SH3BP2
WFS1
NELFA
SLBP
ACOX3
CPZ
NOP14
FAM193A
KIAA0232
WDR1
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
MXD4
CPLX1
SLC26A1
MAN2B2
NSG1
STX18
FGFRL1
CYTL1
SH3TC1
PIGG
BLOC1S4
STK32B
LYAR
SLC2A9
TBC1D14
SORCS2
UVSSA
ZFYVE28
AFAP1
TNIP2
HAUS3
MFSD7
TMEM175
ABLIM2
TMEM128
TMEM129
MRFAP1
TADA2B
HTRA3
MRFAP1L1
EVC2
OTOP1
JAKMIP1
FAM53A
TRMT44
ZBTB49
CCDC96
CRIPAK
DOK7
RNF212
NAT8L
POLN
C4orf48
DEFB131
USP17L24
USP17L25
USP17L26
USP17L5
USP17L27
USP17L28
USP17L29
USP17L30
PSAPL1
USP17L10
USP17L11
USP17L12
USP17L13
USP17L17
USP17L18
USP17L19
USP17L20
USP17L21
USP17L22
MIR548I2
MIR378D1
MIR4800
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2p21.

Table S63.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
EML4
RN7SL414P
SLC3A1
snoU13|ENSG00000239052.1
RN7SKP66
SNORD75|ENSG00000221300.1
snoZ247
HNRNPA1P57
ZFP36L2
PPM1B
SIX3
COX7A2L
PREPL
LRPPRC
SIX2
HAAO
DYNC2LI1
SRBD1
MTA3
THADA
ABCG5
ABCG8
CAMKMT
PKDCC
PLEKHH2
OXER1
KCNG3
C2orf91
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q22.1.

Table S64.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ERCC3
snoU13|ENSG00000238662.1
RN7SKP152
RN7SL455P
RNA5SP111
RNA5SP110
SNORA70F
FIGN
RNA5SP109
GCA
snoU13|ENSG00000238570.1
TBR1
RN7SL423P
MIR4785
RMRPP3
MARCH7
snoZ5
RN7SL393P
RN7SKP281
GALNT5
snoU13|ENSG00000238481.1
snoU13|ENSG00000238543.1
RNA5SP107
SNORD56|ENSG00000200377.1
ARL5A
RN7SL124P
SNORA48|ENSG00000212181.1
RNA5SP106
snoU13|ENSG00000238860.1
snR65|ENSG00000253036.1
TEX41
RN7SL283P
SNORA72|ENSG00000206901.1
RN7SKP286
NXPH2
RNA5SP105
RN7SKP141
SNORA40|ENSG00000208308.1
snoU13|ENSG00000238337.1
MIR5590
RNA5SP104
RN7SKP93
RN7SKP154
RN7SKP103
RN7SL701P
MIR4784
CYP4F31P
SCARNA4|ENSG00000252829.2
CYP4F30P
CFC1
POTEI
CYP4F43P
snoU13|ENSG00000238546.1
RNA5SP103
RN7SL206P
RNY4P7
RNA5SP102
RN7SKP102
snoU13|ENSG00000238341.1
RNU4ATAC
ACVR1
ACVR2A
BIN1
RND3
CACNB4
CCNT2
DARS
DPP4
FAP
GALNT3
GCG
GLI2
GPD2
GPR17
GPR39
GRB14
GYPC
HNMT
INHBB
ITGB6
KCNJ3
KIF5C
LCT
LY75
MCM6
MGAT5
MYO7B
NEB
NR4A2
ORC4
POLR2D
PROC
RBMS1
SCN1A
SCN2A
SCN3A
SCN7A
SCN9A
TNFAIP6
TSN
CXCR4
PKP4
B3GALT1
KYNU
NMI
HS6ST1
CYTIP
ZEB2
CD302
TANK
PSMD14
STAM2
MAP3K2
COBLL1
PLA2R1
RAB3GAP1
UBXN4
CLASP1
R3HDM1
EPC2
PTPN18
MMADHC
C2orf27A
TFCP2L1
BAZ2B
ARHGEF4
LRP1B
PLEKHB2
RIF1
WDR33
SMPD4
PRPF40A
IWS1
LIMS2
MBD5
ARHGAP15
RPRM
UGGT1
SLC4A10
ERMN
IFIH1
SAP130
GTDC1
TTC21B
CSRNP3
MZT2B
MAP3K19
THSD7B
TMEM163
AMMECR1L
ZRANB3
RAB6C
CCDC115
MKI67IP
SFT2D3
FLJ14816
TANC1
KCNH7
CCDC74A
CCDC74B
DAPL1
IMP4
TUBA3E
TUBA3D
FMNL2
GALNT13
LYPD1
XIRP2
CNTNAP5
ACMSD
FAM168B
ACVR1C
LYPD6
LYPD6B
CCDC148
ARL6IP6
SLC38A11
WDSUB1
UPP2
AMER3
SPOPL
CYP27C1
NCKAP5
GPR148
RBM43
C2orf27B
POTEE
ANKRD30BL
CFC1B
POTEJ
MZT2A
POTEF
MIR663B
MIR3679
MIR4783
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q14.13.

Table S65.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
LCP1
RB1
LHFP
ATXN8OS
RNY3P10
RN7SL761P
LINC00364
LINC00355
LINC00395
LINC00448
LINC00459
LINC00358
RNY4P31
RNY3P5
LINC00378
RNA5SP31
LINC00434
RNY4P28
RN7SL375P
RNY4P29
RNA5SP30
RN7SKP6
snoU13|ENSG00000238455.1
LINC00458
LINC00558
RN7SL618P
SUGT1
LINC00345
RNY4P24
RN7SL413P
RNY1P6
RN7SL320P
RPS4XP16
LINC00371
RNA5SP29
RNA5SP28
DLEU7
RNY4P9
RNY4P30
RNY3P2
LINC00462
LINC00441
LINC00562
LINC00444
RN7SL700P
LINC00563
RN7SKP5
snoU13|ENSG00000238483.1
RN7SL288P
RNA5SP27
SNORA31|ENSG00000199477.1
SNORA31|ENSG00000253051.1
7SK|ENSG00000271818.1
RN7SKP3
RN7SL49P
LINC00330
snoU13|ENSG00000238932.1
TSC22D1
LINC00284
LINC00400
RN7SL515P
MIR5006
KBTBD7
snoU13|ENSG00000238651.1
RN7SL597P
SUGT1P3
TPTE2P5
SLC25A15
LINC00598
RN7SKP2
RNY3P9
LINC00332
SNORD116|ENSG00000212553.1
RNY4P14
snoU13|ENSG00000238408.1
LINC00366
LINC00571
RNA5SP26
RN7SKP1
ARL2BPP3
DCLK1
LINC00445
LINC00457
ATP7B
RCBTB2
CPB2
ELF1
ESD
FOXO1
MLNR
GTF2F2
GUCY1B2
HTR2A
KPNA3
MAB21L1
SMAD9
NEK3
PCDH8
PCDH9
RFXAP
TPT1
TRPC4
TNFSF11
SUCLA2
CCNA1
ITM2B
MTRF1
UTP14C
LPAR6
TRIM13
MRPS31
DLEU1
OLFM4
POSTN
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
VWA8
ZC3H13
SPG20
LRCH1
INTS6
CKAP2
NUFIP1
NBEA
PCDH17
RGCC
MED4
DNAJC15
ALG5
VPS36
PHF11
UFM1
ENOX1
RCBTB1
NUDT15
KIAA1704
SUPT20H
THSD1
CYSLTR2
SPRYD7
COG6
KLHL1
PCDH20
SMIM2
NAA16
RNASEH2B
DHRS12
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
EBPL
KBTBD6
EPSTI1
ARL11
WDFY2
CSNK1A1L
PRR20A
FAM216B
LACC1
HNRNPA1L2
DGKH
CCDC122
STOML3
FAM194B
SPERT
FAM124A
LRRC63
SLC25A30
SIAH3
KCNRG
FREM2
NEK5
KCTD4
NHLRC3
SERP2
SERTM1
DLEU2
ALG11
SERPINE3
MIR621
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
MIR759
MIR320D1
MIR3168
MIR4305
MIR3169
MIR3613
SPG20OS
SOHLH2
MIR4704
MIR548X2
MIR4703
MIR5007
MIR5693
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 23 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 0.06 -3.13 1 0.25 8.51 0
1q 1195 0.18 2.96 0.00785 0.17 2.45 0.0226
2p 624 0.18 -0.762 1 0.02 -8.61 1
2q 967 0.18 1.07 0.419 0.02 -7.35 1
3p 644 0.11 -4.17 1 0.14 -2.9 1
3q 733 0.15 -1.79 1 0.10 -4.4 1
4p 289 0.03 -8.45 1 0.32 4.06 9.98e-05
4q 670 0.04 -6.73 1 0.30 5.63 4.04e-08
5p 183 0.16 -4.03 1 0.17 -3.47 1
5q 905 0.10 -3.51 1 0.21 2.46 0.0226
6p 710 0.20 0.687 0.672 0.10 -4.38 1
6q 556 0.18 -1.02 1 0.13 -3.59 1
7p 389 0.55 16.3 0 0.02 -7.05 1
7q 783 0.50 17.6 0 0.02 -6.18 1
8p 338 0.36 4.91 2.72e-06 0.50 12.1 0
8q 551 0.51 15.4 0 0.18 -1.05 1
9p 301 0.20 -1.6 1 0.15 -3.8 1
9q 700 0.17 -0.806 1 0.15 -2.09 1
10p 253 0.09 -6.94 1 0.18 -3.11 1
10q 738 0.06 -6.4 1 0.17 -0.494 1
11p 509 0.13 -4.09 1 0.14 -3.58 1
11q 975 0.13 -1.59 1 0.16 0.298 0.981
12p 339 0.23 -0.0632 1 0.13 -4.32 1
12q 904 0.21 2.7 0.0154 0.14 -1.42 1
13q 560 0.58 19.6 0 0.07 -4.78 1
14q 938 0.11 -2.32 1 0.33 9.64 0
15q 810 0.04 -6.06 1 0.36 10 0
16p 559 0.25 2.38 0.0322 0.10 -5.02 1
16q 455 0.24 1.35 0.278 0.09 -5.65 1
17p 415 0.09 -4.55 1 0.57 17.5 0
17q 972 0.21 2.67 0.0154 0.18 1.39 0.225
18p 104 0.09 -5.19 1 0.60 16.2 0
18q 275 0.07 -5.33 1 0.62 18.9 0
19p 681 0.17 -1.14 1 0.12 -3.49 1
19q 935 0.19 1.73 0.144 0.11 -2.8 1
20p 234 0.58 15.2 0 0.29 1.62 0.154
20q 448 0.71 24.5 0 0.16 -1.83 1
21q 258 0.07 -7.02 1 0.29 2.49 0.0226
22q 564 0.04 -6.98 1 0.33 6.74 4.14e-11
Xp 418 0.16 -2.82 1 0.18 -1.83 1
Xq 668 0.18 -0.531 1 0.16 -1.8 1
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/COAD-TP/19076143/GDAC_MergeDataFiles_12183472/COAD-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 450 Input Tumor Samples.

Tumor Sample Names
TCGA-3L-AA1B-01A-11D-A36W-01
TCGA-4N-A93T-01A-11D-A36W-01
TCGA-4T-AA8H-01A-11D-A40O-01
TCGA-5M-AAT4-01A-11D-A40O-01
TCGA-5M-AAT5-01A-21D-A40O-01
TCGA-5M-AAT6-01A-11D-A40O-01
TCGA-5M-AATA-01A-31D-A40O-01
TCGA-5M-AATE-01A-11D-A40O-01
TCGA-A6-2671-01A-01D-1549-01
TCGA-A6-2672-01A-01D-1549-01

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.

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)
[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)
[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)