SNP6 Copy number analysis (GISTIC2)
Colon Adenocarcinoma (Primary solid tumor)
15 July 2014  |  analyses__2014_07_15
Maintainer Information
Citation Information
doi:10.7908/C1PR7TPD
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1PR7TPD
Overview
Introduction

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

Summary

There were 438 tumor samples used in this analysis: 23 significant arm-level results, 23 significant focal amplifications, and 46 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 - 23 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 3.2555e-41 3.937e-22 chr20:26197900-30582729 26
20q12 7.1705e-37 2.7277e-21 chr20:39751003-40360023 6
13q12.13 8.7972e-26 1.1582e-19 chr13:27521847-27533641 0 [USP12]
8q24.21 1.786e-19 7.1889e-19 chr8:128389850-128754688 3
17q12 3.1317e-14 1.7012e-13 chr17:37837542-38021723 6
8p11.23 2.449e-12 1.1649e-09 chr8:38170522-38237581 1
11p15.5 2.486e-09 2.486e-09 chr11:2141587-2244703 8
12p13.33 3.0405e-08 3.0405e-08 chr12:2055585-4699385 23
13q22.1 2.308e-12 9.1531e-08 chr13:73599695-74055302 1
5q22.3 4.5556e-06 4.5556e-06 chr5:114756122-114759166 0 [FEM1C]
8p11.21 3.6506e-10 1.7554e-05 chr8:41614677-42365372 9
20q13.32 2.3398e-06 0.00033196 chr20:51514873-59641966 64
6p21.1 0.0029385 0.0029385 chr6:40092319-44407505 90
19q13.11 0.0059707 0.0059707 chr19:32351550-33019554 3
8q12.1 0.0001819 0.012511 chr8:42932479-70211670 103
19p13.2 0.025339 0.025339 chr19:7300056-7398264 0 [INSR]
5p13.2 0.026254 0.026254 chr5:27059148-50133343 91
20p11.23 0.0062115 0.035539 chr20:19045837-20680922 8
16p11.2 0.032159 0.079045 chr16:30611431-30720446 4
2q33.1 0.093562 0.093562 chr2:199627908-199644614 0 [SATB2]
17q24.1 0.0027062 0.094101 chr17:63179119-69202774 39
17p11.2 0.044058 0.10558 chr17:21124724-21305391 3
16q12.1 0.071969 0.17893 chr16:51079810-53017796 5
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
hsa-mir-3193
BCL2L1
FOXS1
ID1
TPX2
REM1
HM13
PDRG1
COX4I2
MYLK2
DEFB118
DUSP15
MLLT10P1
LINC00028
TTLL9
DEFB115
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
FRG1B
XKR7
PSIMCT-1
MIR3193
Genes in Wide Peak

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

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

Genes
TOP1
PLCG1
ZHX3
LPIN3
CHD6
EMILIN3
Genes in Wide Peak

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

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

Genes
MYC
POU5F1B
LOC727677
Genes in Wide Peak

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

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

Genes
ERBB2
GRB7
IKZF3
MIEN1
PGAP3
MIR4728
Genes in Wide Peak

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

Table S5.  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 11p15.5.

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

Genes
hsa-mir-483
IGF2
INS
TH
IGF2-AS1
MIR483
INS-IGF2
MIR4686
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
CACNA1C
FGF6
FKBP4
FOXM1
TEAD4
TULP3
FGF23
DYRK4
RAD51AP1
TSPAN9
ITFG2
PRMT8
PARP11
C12orf4
C12orf5
C12orf32
NRIP2
EFCAB4B
DCP1B
LOC283440
LOC100507424
LOC100652846
Genes in Wide Peak

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

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

Genes
KLF5
Genes in Wide Peak

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

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

Genes
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 20q13.32.

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

Genes
GNAS
hsa-mir-646
hsa-mir-298
hsa-mir-4325
ATP5E
BMP7
CSTF1
CTSZ
CYP24A1
EDN3
MC3R
PCK1
PFDN4
PPP1R3D
AURKA
TFAP2C
ZNF217
RAE1
BCAS1
STX16
VAPB
SYCP2
SPO11
SLMO2
TH1L
C20orf43
PPP4R1L
RBM38
DOK5
PMEPA1
CASS4
RAB22A
CDH26
FAM217B
NPEPL1
TUBB1
ZBP1
FAM210B
PHACTR3
TSHZ2
C20orf85
ZNF831
GCNT7
CBLN4
CTCFL
LOC149773
GNAS-AS1
APCDD1L
FAM209A
C20orf197
LOC284757
FAM209B
SUMO1P1
MIR296
MIR298
MIR4325
MTRNR2L3
LOC100506384
SLMO2-ATP5E
STX16-NPEPL1
MIR4756
MIR4532
MIR4533
MIR5095
Genes in Wide Peak

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

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

Genes
CCND3
TFEB
BYSL
CDC5L
SLC29A1
GUCA1A
GUCA1B
HSP90AB1
MDFI
MEA1
NFKBIE
NFYA
PEX6
PGC
POLH
PPP2R5D
PTK7
PRPH2
SRF
TBCC
VEGFA
NCR2
MED20
POLR1C
MAD2L1BP
CUL7
C6orf108
CNPY3
FRS3
SLC22A7
APOBEC2
CAPN11
CUL9
UBR2
KIAA0240
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
TCTE1
SPATS1
C6orf223
RSPH9
LRRC73
TREML2P1
LOC221442
C6orf130
TSPO2
UNC5CL
TREML4
RPL7L1
TREML1
TREML3
SLC35B2
FLJ41649
CRIP3
C6orf226
TMEM151B
ATP6V0CP3
C6orf132
TDRG1
LOC100132354
TOMM6
MIR4647
MIR4641
MIR4642
Genes in Wide Peak

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

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

Genes
ZNF507
DPY19L3
LOC400684
Genes in Wide Peak

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

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

Genes
PLAG1
TCEA1
CHCHD7
hsa-mir-124-2
ASPH
CA8
CEBPD
CRH
CYP7A1
FNTA
NPBWR1
LYN
MCM4
MOS
MYBL1
OPRK1
PDE7A
PENK
PRKDC
RAB2A
RP1
RPS20
SDCBP
SNAI2
TTPA
UBE2V2
NSMAF
RGS20
GGH
CYP7B1
MTFR1
ST18
TOX
RB1CC1
LYPLA1
ARFGEF1
COPS5
RRS1
KIAA0146
SGK3
C8orf71
PTTG3P
SNORD54
BHLHE22
MRPL15
ATP6V1H
SNTG1
IMPAD1
ARMC1
CHD7
C8orf44
CPA6
SOX17
EFCAB1
CSPP1
VCPIP1
PREX2
SGK196
TRIM55
DNAJC5B
FAM110B
TGS1
XKR4
PCMTD1
C8orf34
TMEM68
ADHFE1
UBXN2B
PXDNL
HGSNAT
C8orf45
CLVS1
SDR16C5
YTHDF3
C8orf46
LOC286177
NKAIN3
LOC286184
LOC286186
PPP1R42
LOC286189
POTEA
FAM150A
LOC401463
MIR124-2
C8orf22
LINC00293
LINC00251
SNHG6
SNORD87
UG0898H09
TCF24
LOC100130155
LOC100130298
SBF1P1
LOC100287846
LOC100505659
LOC100505676
LOC100505718
LOC100507632
LOC100507651
C8orf44-SGK3
MIR4470
Genes in Wide Peak

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

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

Genes
LIFR
hsa-mir-1274a
hsa-mir-580
hsa-mir-579
hsa-mir-4279
C6
C7
C9
CDH6
DAB2
FGF10
FYB
GDNF
GHR
HMGCS1
IL7R
NPR3
OXCT1
PRKAA1
PRLR
PTGER4
RAD1
RPL37
SEPP1
SKP2
SLC1A3
TARS
ZNF131
OSMR
NUP155
PAIP1
MRPS30
SUB1
PDZD2
NNT
TTC33
AMACR
NIPBL
RAI14
FBXO4
DROSHA
SLC45A2
RXFP3
ZFR
MTMR12
WDR70
BRIX1
C5orf22
CCL28
GOLPH3
C5orf28
AGXT2
C5orf42
PARP8
SPEF2
ADAMTS12
CARD6
LMBRD2
C1QTNF3
EMB
HEATR7B2
EGFLAM
NADKD1
UGT3A1
CAPSL
DNAJC21
TTC23L
LOC153684
UGT3A2
NIM1
RANBP3L
RICTOR
C5orf51
LOC340113
PLCXD3
HCN1
C5orf34
C5orf39
SNORD72
LOC643401
LOC646719
LOC648987
MIR580
LOC729862
CCDC152
LOC100132356
MIR4279
MIR3650
LOC100506548
C1QTNF3-AMACR
EGFLAM-AS4
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20p11.23.

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

Genes
INSM1
C20orf26
NAA20
CRNKL1
RIN2
RALGAPA2
SLC24A3
LOC100130264
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
ZNF689
Genes in Wide Peak

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

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

Genes
PRKAR1A
hsa-mir-635
hsa-mir-548d-2
hsa-mir-634
APOH
CACNG1
BPTF
KCNJ2
KCNJ16
KPNA2
PRKCA
MAP2K6
PSMD12
AXIN2
RGS9
SLC16A6
HELZ
ABCA10
ABCA9
ABCA8
ARSG
ABCA6
ABCA5
NOL11
PITPNC1
CACNG5
CACNG4
AMZ2
FAM20A
WIPI1
CEP112
C17orf58
KCNJ2-AS1
LOC440461
MIR634
MIR635
SNORA38B
LOC100499466
MIR4524A
Genes in Wide Peak

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

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

Genes
KCNJ12
MAP2K3
C17orf103
Genes in Wide Peak

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

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

Genes
SALL1
TOX3
LOC388276
LOC643714
LOC100505619

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 - 46 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 4.1302e-119 4.1302e-119 chr16:5144019-7771745 1
6q26 4.2626e-42 4.2626e-42 chr6:161693099-163153207 1
20p12.1 2.8457e-41 2.8457e-41 chr20:14302876-15179819 2
4q22.1 1.0125e-40 3.2691e-38 chr4:91148280-93240505 1
16q23.1 1.2645e-32 1.2645e-32 chr16:78129058-79627770 1
1p33 1.4633e-33 6.0757e-30 chr1:49193395-50514967 1
3p14.2 7.4552e-31 1.3344e-29 chr3:59034763-61547330 1
5q11.2 1.4974e-25 5.8402e-23 chr5:58260298-59787985 3
18q21.2 1.3653e-24 8.1019e-20 chr18:48472083-48705371 2
1p36.11 3.1825e-23 3.3189e-19 chr1:26527443-27650365 25
6p25.3 1.2978e-18 1.2978e-18 chr6:1608837-2252425 2
3q26.31 1.1721e-15 1.1721e-15 chr3:173999806-175760559 2
4q35.1 2.9803e-18 4.9521e-15 chr4:178911874-186507186 38
10q21.1 1.9002e-16 1.0986e-14 chr10:53057593-53461574 3
8p22 5.8927e-15 2.9093e-12 chr8:15092726-16024383 1
10q23.31 8.6176e-14 7.4335e-09 chr10:89313008-90034038 5
5q21.3 1.1555e-17 2.4816e-07 chr5:96090301-107194910 22
7q31.1 2.4444e-05 2.472e-05 chr7:109599468-111366370 2
19p13.3 5.137e-05 5.137e-05 chr19:1033227-1907478 36
21q11.2 7.2131e-05 7.2131e-05 chr21:1-26218513 44
15q22.33 3.8585e-05 0.00013222 chr15:67067796-67494822 1
15q11.2 1.4113e-08 0.00027743 chr15:1-27218028 136
5q23.1 3.0863e-11 0.00034124 chr5:104425581-122696881 63
18q12.2 1.4782e-13 0.00034124 chr18:35235531-39060470 4
17p12 0.00048583 0.00048014 chr17:10740609-12456081 6
8p23.3 3.9909e-10 0.001116 chr8:1-6262191 15
22q13.32 0.0011824 0.0011919 chr22:48668761-49176545 5
18p11.31 0.013139 0.012672 chr18:3277692-5144550 5
18q22.1 4.9569e-14 0.0276 chr18:63200038-71367031 15
9p21.3 0.029825 0.029768 chr9:21512064-22448737 7
14q31.1 0.037319 0.038916 chr14:58330395-107349540 482
10q25.2 4.6879e-07 0.041065 chr10:100989718-135534747 303
15q15.2 3.0294e-08 0.045941 chr15:37383162-44170698 110
15q21.1 6.1135e-07 0.057773 chr15:44851245-45299932 5
3p26.1 0.0049508 0.060326 chr3:1-21447833 133
8p11.21 0.050414 0.060326 chr8:42883855-47753079 4
17q24.3 0.082889 0.084515 chr17:68173089-70595192 2
12p13.2 0.10892 0.10492 chr12:6885077-16704356 172
1q43 0.13027 0.13027 chr1:229792777-240171058 64
4p16.2 0.14052 0.14227 chr4:1-42412686 249
2q32.1 0.1479 0.14706 chr2:120935779-243199373 741
10p15.3 0.17518 0.17518 chr10:1-26225233 155
1p13.1 0.00077572 0.19722 chr1:55347880-149898950 499
13q14.13 0.21206 0.21695 chr13:34539992-72013697 159
2p21 0.21957 0.22329 chr2:40738978-45880121 27
20p12.1 2.8457e-41 1 chr20:1-63025520 672
Genes in Wide Peak

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

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

Genes
RBFOX1
Genes in Wide Peak

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

Table S21.  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 20p12.1.

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

Genes
FLRT3
MACROD2-AS1
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
FAM190A
Genes in Wide Peak

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

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

Genes
WWOX
Genes in Wide Peak

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

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

Genes
BEND5
Genes in Wide Peak

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

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

Genes
FHIT
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q11.2.

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

Genes
hsa-mir-582
PDE4D
PART1
Genes in Wide Peak

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

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

Genes
SMAD4
ELAC1
Genes in Wide Peak

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

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

Genes
ARID1A
hsa-mir-1976
CD52
SFN
HMGN2
RPS6KA1
SLC9A1
NR0B2
NUDC
WDTC1
GPN2
AIM1L
PIGV
GPATCH3
CEP85
LIN28A
DHDDS
SH3BGRL3
ZDHHC18
UBXN11
FAM46B
C1orf172
ZNF683
TRNP1
MIR1976
Genes in Wide Peak

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

Table S30.  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 3q26.31.

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

Genes
NAALADL2
MIR4789
Genes in Wide Peak

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

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

Genes
hsa-mir-1305
SLC25A4
CASP3
DCTD
ACSL1
ING2
IRF2
PDLIM3
CLDN22
UFSP2
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
TRAPPC11
MLF1IP
WWC2
SNX25
MGC45800
ENPP6
C4orf38
RWDD4
CCDC111
CCDC110
ANKRD37
LOC389247
HELT
FAM92A3
C4orf47
SLED1
LINC00290
LOC728175
LOC731424
CLDN24
MIR1305
MIR3945
LOC100506229
Genes in Wide Peak

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

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

Genes
hsa-mir-605
CSTF2T
MIR605
Genes in Wide Peak

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

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

Genes
TUSC3
Genes in Wide Peak

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

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

Genes
PTEN
PAPSS2
ATAD1
CFL1P1
KLLN
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q21.3.

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

Genes
hsa-mir-548p
CHD1
EFNA5
LNPEP
PAM
ST8SIA4
RAB9BP1
PPIP5K2
ERAP1
GIN1
RIOK2
ERAP2
NUDT12
C5orf30
SLCO6A1
LIX1
RGMB
FAM174A
SLCO4C1
FLJ35946
LOC100133050
LOC100289230
Genes in Wide Peak

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

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

Genes
LRRN3
IMMP2L
Genes in Wide Peak

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

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

Genes
STK11
TCF3
hsa-mir-1909
ATP5D
CIRBP
EFNA2
GAMT
GPX4
POLR2E
RPS15
APC2
ABCA7
UQCR11
SBNO2
HMHA1
DAZAP1
MBD3
PCSK4
C19orf24
REXO1
FAM108A1
KLF16
MUM1
MIDN
REEP6
PLK5
CIRBP-AS1
C19orf25
ATP8B3
C19orf26
ADAMTSL5
NDUFS7
ONECUT3
MEX3D
LOC100288123
MIR1909
Genes in Wide Peak

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

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

Genes
hsa-mir-548x
hsa-mir-125b-2
hsa-let-7c
hsa-mir-3118-5
hsa-mir-3156-3
BAGE
CXADR
NCAM2
TMPRSS15
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
CHODL-AS1
C21orf15
LINC00308
C21orf91
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
CHODL
ANKRD30BP2
LIPI
ABCC13
C21orf91-OT1
D21S2088E
POTED
LINC00317
LINC00320
LOC388813
LINC00478
ANKRD20A11P
MIRLET7C
MIR125B2
MIR99A
TEKT4P2
MIR3156-3
MIR3687
MIR3648
C21orf37
Genes in Wide Peak

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

Table S40.  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 15q11.2.

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

Genes
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
NBEAP1
GABRA5
GABRB3
IPW
NDN
SNRPN
UBE3A
MKRN3
PAR5
SNURF
CYFIP1
C15orf2
MAGEL2
ATP10A
NIPA2
SNORD107
TUBGCP5
NIPA1
PAR1
LOC283683
OR4N4
HERC2P3
GOLGA6L1
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
SNORD64
PAR4
PAR-SN
LOC348120
GOLGA8E
OR4M2
OR4N3P
HERC2P2
NF1P2
LOC503519
CHEK2P2
LOC646214
CXADRP2
REREP3
LOC653061
SNORD116-19
GOLGA6L6
LOC727924
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
LOC100128714
HERC2P7
GOLGA8DP
MIR4509-1
MIR4509-2
MIR4508
MIR4509-3
MIR4715
Genes in Wide Peak

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

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

Genes
APC
hsa-mir-1244-2
hsa-mir-548f-3
CAMK4
CDO1
AP3S1
DMXL1
EFNA5
FER
HSD17B4
KCNN2
LOX
MAN2A1
MCC
PGGT1B
PPIC
SNX2
SRP19
REEP5
ATG12
NREP
RAB9BP1
SNCAIP
PJA2
TNFAIP8
SNX24
TMED7
PRR16
COMMD10
FLJ11235
TRIM36
FEM1C
SEMA6A
EPB41L4A
FBXL17
YTHDC2
TSSK1B
TSLP
SLC25A46
PRDM6
FTMT
EPB41L4A-AS1
ZNF474
STARD4
WDR36
SRFBP1
CCDC112
DCP2
AQPEP
DTWD2
FAM170A
TICAM2
TMEM232
LOC644100
SNORA13
LOC728342
LOC100289673
MIR1244-1
TMED7-TICAM2
MIR1244-3
MIR1244-2
LOC100505678
LOC100505841
Genes in Wide Peak

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

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

Genes
hsa-mir-924
hsa-mir-4318
LOC647946
MIR4318
Genes in Wide Peak

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

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

Genes
MAP2K4
hsa-mir-744
DNAH9
ZNF18
SHISA6
MIR744
Genes in Wide Peak

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

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

Genes
hsa-mir-596
CLN8
MYOM2
DLGAP2
ARHGEF10
KBTBD11
FBXO25
CSMD1
C8orf42
ERICH1
ZNF596
LOC286083
OR4F21
RPL23AP53
MIR596
Genes in Wide Peak

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

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

Genes
hsa-mir-3201
FAM19A5
LOC284933
MIR3201
MIR4535
Genes in Wide Peak

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

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

Genes
TGIF1
DLGAP1
LOC201477
LOC284215
FLJ35776
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q22.1.

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

Genes
CDH7
SOCS6
CD226
RTTN
CDH19
TMX3
CCDC102B
NETO1
DSEL
CBLN2
DOK6
LOC400655
LOC643542
LOC100505776
LOC100505817
Genes in Wide Peak

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

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

Genes
hsa-mir-31
CDKN2A
CDKN2B
MTAP
C9orf53
MIR31
CDKN2B-AS1
Genes in Wide Peak

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

Table S50.  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
hsa-mir-203
hsa-mir-4309
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-345
hsa-mir-342
hsa-mir-3173
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
SERPINA3
ACTN1
ACYP1
ARG2
BDKRB1
BDKRB2
ZFP36L1
CALM1
SERPINA6
ENTPD5
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
ELK2AP
EML1
ERH
ESR2
ESRRB
FNTB
FOS
FUT8
GALC
GPX2
GSTZ1
GTF2A1
BRF1
HIF1A
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LTBP2
MARK3
MAX
ATXN3
MAP3K9
ALDH6A1
MNAT1
MTHFD1
NDUFB1
SIX6
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPM1A
PPP2R5C
PPP2R5E
PRKCH
LGMN
PSEN1
PSMA3
PSMC1
ABCD4
RAD51B
MOK
ARID4A
RTN1
SEL1L
SRSF5
SIX1
SLC8A3
SLC10A1
SNAPC1
SPTB
TGFB3
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
ZBTB25
DPF3
GPR68
GPR65
NUMB
ADAM21
ADAM20
ADAM6
DLK1
CCNK
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
NRXN3
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
KIAA0586
KIAA0125
KIAA0317
TECPR2
MED6
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
C14orf1
VASH1
ZBTB1
SNW1
PCNX
DAAM1
TTLL5
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
C14orf109
PLEK2
TIMM9
MLH3
KCNH5
PRO1768
GPR132
POMT2
COQ6
FCF1
RDH11
SERPINA10
GLRX5
COX16
DACT1
ATP6V1D
EVL
C14orf129
JKAMP
CINP
DHRS7
ASB2
SIX4
ZFYVE1
CPSF2
KCNK10
CDCA4
C14orf102
ATG2B
UBR7
EXD2
VRTN
SYNJ2BP
SLC39A9
MEG3
FLVCR2
C14orf118
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
ACTR10
YLPM1
KCNK13
C14orf162
C14orf132
DDX24
ADCK1
TMEM63C
RHOJ
GALNTL1
PLEKHH1
TRMT5
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
C14orf133
SMOC1
MOAP1
DIO3OS
IRF2BPL
MPP5
INF2
C14orf135
GPR135
OTUB2
ZFYVE21
MEG8
WDR25
LINC00341
ZC2HC1C
C14orf169
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
C14orf45
TMEM121
SGPP1
AMN
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
CHURC1
C14orf43
LIN52
NEK9
EXOC3L4
WDR20
IFT43
WDR89
C14orf149
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
LINC00239
LOC145216
RDH12
ADAM21P1
GSC
SERPINA12
PRIMA1
PPP1R36
SLC38A6
C14orf37
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
C14orf49
TMEM30B
SAMD15
EML5
MGC23270
NUDT14
LINC00521
SERPINA11
PROX2
ZDHHC22
TMED8
C14orf178
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
KIAA0284
C14orf80
C14orf55
C14orf39
CCDC85C
ITPK1-AS1
SNORD56B
SERPINA9
LINC00226
LINC00221
VSX2
COX8C
ASPG
RAB15
FLJ31306
TOMM20L
SERPINA13
C14orf64
RTL1
TMEM179
HEATR4
FLJ22447
PLEKHD1
LOC400236
LOC400238
DICER1-AS1
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
LINC00238
CCDC88C
TEX21P
MIR323A
MIR337
MIR345
MIR376C
MIR369
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR323B
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
LOC645431
FLJ43390
SYNDIG1L
TEX22
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORA79
MIR411
MIR654
MIR655
MIR656
C14orf38
LOC731223
SNORD113-1
SNORD113-2
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
LOC100129345
LOC100131366
LOC100289511
MIR1247
MIR1185-1
MIR1185-2
MIR1260A
MIR1197
MIR1193
MIR4309
MIR3173
LOC100506321
LOC100507043
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR3545
MIR4708
MIR4709
MIR4710
MIR4706
MIR2392
LOC100628307
HIF1A-AS2
Genes in Wide Peak

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

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

Genes
FGFR2
TLX1
NFKB2
DUX4
SUFU
hsa-mir-202
hsa-mir-378c
hsa-mir-4297
hsa-mir-4296
hsa-mir-2110
hsa-mir-4295
hsa-mir-548e
hsa-mir-609
hsa-mir-936
hsa-mir-1307
hsa-mir-146b
hsa-mir-3158-1
hsa-mir-608
ACADSB
ADAM8
ADD3
ADRA2A
ADRB1
ARL3
BNIP3
CASP7
CHUK
ABCC2
COL17A1
COX15
CPN1
CTBP2
CYP2E1
CYP17A1
DMBT1
DOCK1
DUSP5
ECHS1
EMX2
FGF8
GFRA1
GOT1
PRLHR
GPR26
GRK5
HABP2
HMX2
INPP5A
ABLIM1
MGMT
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
HTRA1
PSD
PTPRE
RGS10
SCD
FBXW4
SLC18A2
TAF5
TCF7L2
TECTB
TIAL1
UROS
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
EIF3A
GBF1
LDB1
BTRC
PKD2L1
INA
SMC3
NEURL
BUB3
NOLC1
GSTO1
BAG3
SH3PXD2A
FAM53B
SLK
DCLRE1A
ACTR1A
SMNDC1
NPM3
GLRX3
DPYSL4
TACC2
ERLIN1
LBX1
MGEA5
TUBGCP2
PRDX3
VAX1
ATE1
SEC23IP
RAB11FIP2
INPP5F
NT5C2
PDCD11
SORCS3
PPRC1
FAM175B
DNMBP
DPCD
SEC31B
ATRNL1
C10orf137
CNNM1
DUX2
PDCD4
VENTX
POLL
KCNIP2
CUZD1
CALY
CALHM2
CUTC
CHST15
ACSL5
ZRANB1
TTC40
NSMCE4A
CNNM2
C10orf26
C10orf118
CWF19L1
HIF1AN
WDR11
FAM178A
DHX32
PPP2R2D
FAM45B
TDRD1
BCCIP
C10orf2
ENTPD7
AS3MT
GPAM
KIAA1598
FAM160B1
SEMA4G
PLEKHA1
FAM204A
LHPP
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
TMEM180
MCMBP
C10orf95
C10orf81
PDZD7
OBFC1
C10orf88
WDR96
LRRC27
TRIM8
KAZALD1
SFXN3
SLC25A28
ELOVL3
PCGF6
GPR123
LZTS2
NKX6-2
MRPL43
AFAP1L2
USMG5
KNDC1
ITPRIP
LINC00263
MTG1
BBIP1
FANK1
SYCE1
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
MMP21
SFXN2
PDZD8
C10orf32
GSTO2
SFR1
CALHM3
CTAGE7P
CLRN3
PNLIPRP3
SFXN4
CPXM2
TRUB1
VTI1A
LOC143188
C10orf82
C10orf46
NKX2-3
CCDC147
C10orf91
PWWP2B
EMX2OS
PPAPDC1A
PAOX
FAM24B
EBF3
CALHM1
CASC2
TCERG1L
HSPA12A
C10orf125
JAKMIP3
STK32C
BLOC1S2
RBM20
LOC282997
LOC283038
LOC283089
KCNK18
VWA2
NANOS1
HMX3
NHLRC2
C10orf96
FLJ46361
ENO4
ARMS2
C10orf122
LOC387723
GUCY2GP
NKX1-2
FLJ41350
C10orf120
LOC399815
METTL10
FLJ37035
FOXI2
FLJ46300
LOC399829
SPRNP1
FAM45A
FRG2B
SPRN
MIR146B
MIR202
NPS
LOC619207
SNORA19
FAM196A
RPL13AP6
DUX4L7
DUX4L6
DUX4L5
DUX4L3
SNORA12
MIR608
MIR609
DUX4L2
LOC729020
TLX1NB
MIR936
LOC100169752
DNMBP-AS1
LOC100289509
MIR1307
MIR2110
MIR378C
MIR4297
MIR3158-1
MIR4295
MIR3158-2
MIR4296
MIR3941
MIR3663
MIR3944
LOC100505761
LOC100505839
LOC100505933
C10orf32-AS3MT
FAM24B-CUZD1
MIR4680
MIR4483
MIR4682
MIR4482-1
MIR4484
MIR4681
Genes in Wide Peak

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

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

Genes
BUB1B
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
CAPN3
CKMT1B
EPB42
GANC
GCHFR
PDIA3
ITPKA
IVD
LTK
MAP1A
MFAP1
PLCB2
RAD51
SPINT1
SRP14
THBS1
TP53BP1
TYRO3
JMJD7-PLA2G4B
SNAP23
TGM5
PPIP5K1
LCMT2
RASGRP1
SERF2
GPR176
CHP
OIP5
BAHD1
MAPKBP1
RTF1
MGA
VPS39
CCNDBP1
C15orf63
TMEM87A
RPAP1
RPUSD2
TUBGCP4
EHD4
NDUFAF1
NUSAP1
SPTBN5
DLL4
INO80
PPP1R14D
HAUS2
FAM82A2
DNAJC17
PAK6
CASC5
STARD9
VPS18
ZFP106
CHAC1
WDR76
TMEM62
ELL3
ZFYVE19
DISP2
C15orf57
C15orf23
BMF
CHST14
TGM7
CATSPER2
PLA2G4E
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
SPRED1
ADAL
EXD1
FSIP1
RHOV
UBR1
PLA2G4F
LRRC57
FAM98B
PLA2G4D
MRPL42P5
C15orf52
C15orf53
C15orf54
EIF2AK4
CATSPER2P1
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
MIR626
MIR627
LOC728758
OIP5-AS1
LOC100131089
ANKRD63
JMJD7
PLA2G4B
MIR1282
MIR4310
LOC100505648
SERF2-C15ORF63
Genes in Wide Peak

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

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

Genes
B2M
SPG11
TRIM69
C15orf43
PATL2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p26.1.

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

Genes
FANCD2
PPARG
RAF1
VHL
XPC
SRGAP3
hsa-mir-3135
hsa-mir-563
hsa-mir-3134
hsa-mir-4270
hsa-mir-885
ATP2B2
BTD
CAV3
DAZL
FBLN2
GRM7
HRH1
IL5RA
IRAK2
ITPR1
OGG1
OXTR
RAB5A
RPL32
SATB1
SEC13
SETMAR
SLC6A1
SLC6A6
SLC6A11
SYN2
TIMP4
NR2C2
WNT7A
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
LSM3
LINC00312
LMCD1
C3orf32
TRNT1
CRBN
C3orf19
GHRL
ARL8B
SETD5
TMEM40
TMEM111
BRK1
RAD18
LRRN1
CIDEC
ZFYVE20
MTMR14
MRPS25
CRELD1
TMEM43
HDAC11
TSEN2
GRIP2
C3orf20
JAGN1
GHRLOS2
IL17RC
EAF1
OXNAD1
C3orf24
GALNTL2
KCNH8
CHCHD4
METTL6
TAMM41
IL17RE
SGOL1
PP2D1
EFHB
CPNE9
FGD5
CIDECP
CNTN4
SUMF1
RPUSD3
PRRT3
LOC285370
LOC285375
DPH3
LOC339862
COL6A4P1
TPRXL
LHFPL4
LOC401052
LOC440944
SNORA7A
MIR563
MIR885
EGOT
GHRLOS
LOC100129480
LOC100132526
LOC100288428
MIR4270
MIR3714
FGD5-AS1
LOC100505696
LOC100507582
ARPC4-TTLL3
MIR4791
MIR4790
Genes in Wide Peak

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

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

Genes
FNTA
SGK196
HGSNAT
POTEA
Genes in Wide Peak

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

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

Genes
SOX9
LOC100499467
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
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
hsa-mir-141
A2M
A2MP1
APOBEC1
ARHGDIB
ART4
C1R
C1S
C3AR1
CD4
CD69
CDKN1B
CREBL2
ATN1
PHC1
EMP1
ENO2
EPS8
GNB3
GPR19
GRIN2B
GUCY2C
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
LRP6
M6PR
MGP
MGST1
OLR1
PDE6H
PRB1
PRB3
PRB4
PRH1
PRH2
PTPN6
PTPRO
PEX5
PZP
SLC2A3
TPI1
MFAP5
USP5
KLRC4
CSDA
GPRC5A
CD163
GDF3
CLSTN3
CLEC2B
LPCAT3
KLRG1
LRRC23
EMG1
LEPREL2
KLRAP1
STRAP
PRR4
PHB2
KLRK1
GABARAPL1
NECAP1
CLEC4E
GPR162
CLEC2D
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
CLEC4A
HEBP1
DERA
DDX47
CLEC1B
CLEC1A
C1RL
KLRF1
WBP11
MANSC1
MAGOHB
FAM90A1
STYK1
GPRC5D
ATF7IP
H2AFJ
FOXJ2
AICDA
RIMKLB
KIAA1467
CLEC7A
BCL2L14
PLBD1
NANOG
DUSP16
APOLD1
GSG1
CDCA3
RBP5
SPSB2
RERG
HTR7P1
CLEC6A
C12orf57
LOH12CR1
C12orf59
HIST4H4
ERP27
SLC2A14
A2ML1
LOC144571
C12orf60
CLEC12A
CLECL1
CLEC4C
DSTNP2
C12orf33
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
MATL2963
CD163L1
RPL13P5
CLEC9A
C12orf36
CLEC4D
LOC338817
ACSM4
TAS2R42
DPPA3
NANOGNB
LOC374443
CLEC2A
CLEC12B
RPL13AP20
LOC389634
MIR141
MIR200C
ZNF705A
FAM66C
DDX12P
C12orf69
LOH12CR2
POU5F1P3
LOC642846
FAM86FP
PRB2
SCARNA12
MIR613
MIR614
SLC15A5
LOC100129361
MIR1244-1
MIR1244-3
MIR1244-2
KLRF2
LOC100499405
LOC100506314
KLRC4-KLRK1
PRH1-PRR4
Genes in Wide Peak

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

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

Genes
hsa-mir-1537
hsa-mir-1182
ACTN2
AGT
LYST
CHRM3
GALNT2
GNG4
KCNK1
LGALS8
MTR
NID1
RYR2
TARBP1
TBCE
GPR137B
TSNAX
GNPAT
GGPS1
TOMM20
CAPN9
COG2
RBM34
DISC2
DISC1
ARID4B
EGLN1
KIAA1383
HEATR1
ERO1LB
SIPA1L2
ZP4
ARV1
TTC13
PGBD5
PCNXL2
C1orf124
NTPCR
KIAA1804
C1orf198
C1orf131
EDARADD
SLC35F3
B3GALNT2
EXOC8
LOC339535
IRF2BP2
FAM89A
C1orf31
TRIM67
SNRPD2P2
SNORA14B
LOC100130331
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
LINC00184
TSNAX-DISC1
LOC100506795
LOC100506810
MIR4753
MIR4671
MIR4427
Genes in Wide Peak

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

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

Genes
FGFR3
WHSC1
PHOX2B
hsa-mir-574
hsa-mir-1255b-1
hsa-mir-4275
hsa-mir-573
hsa-mir-218-1
hsa-mir-572
hsa-mir-3138
hsa-mir-548i-2
hsa-mir-95
hsa-mir-4274
hsa-mir-943
hsa-mir-571
ADD1
ADRA2C
APBB2
RHOH
ATP5I
NKX3-2
BST1
CCKAR
CD38
CRMP1
CTBP1
DGKQ
DHX15
DRD5
EVC
GAK
GRK4
HTT
HGFAC
UBE2K
HMX1
IDUA
RBPJ
LETM1
LRPAP1
MSX1
MYL5
PCDH7
PDE6B
PPP2R2C
QDPR
RFC1
RGS12
RNF4
RPL9
S100P
SH3BP2
SOD3
TLR1
UCHL1
UGDH
WFS1
WHSC2
ZNF141
SLBP
ACOX3
CPZ
NOP14
FAM193A
PROM1
LDB2
SLIT2
RAB28
KIAA0232
WDR1
HS3ST1
FGFBP1
C4orf6
MFSD10
MAEA
TLR6
PCGF3
SPON2
TACC3
SLC30A9
SLC34A2
MXD4
PTTG2
CPLX1
SLC26A1
PPARGC1A
LIAS
LIMCH1
TBC1D1
SEL1L3
PDS5A
MAN2B2
FBXL5
D4S234E
FAM184B
GPR78
ZCCHC4
ANAPC4
LAP3
KLHL5
SEPSECS
KLF3
STX18
FGFRL1
CYTL1
SH3TC1
RBM47
PIGG
DCAF16
TMEM33
LGI2
PGM2
C4orf19
TBC1D19
PI4K2B
CNO
STK32B
CHRNA9
LYAR
N4BP2
SLC2A9
KIAA1239
TBC1D14
SORCS2
CC2D2A
STIM2
KIAA1530
WDR19
ZFYVE28
GBA3
AFAP1
NCAPG
TNIP2
HAUS3
FLJ13197
NSUN7
ABCA11P
TMEM156
GRPEL1
MED28
KCNIP4
TLR10
FGFBP2
MFSD7
TMEM175
ABLIM2
AFAP1-AS1
TMEM128
ZNF518B
CCDC149
C4orf42
TMEM129
FAM114A1
MRFAP1
LOC93622
TADA2B
HTRA3
C1QTNF7
MRFAP1L1
CLNK
ARAP2
CPEB2
EVC2
PACRGL
OTOP1
SHISA3
ZNF595
LOC152742
JAKMIP1
KLB
FAM53A
METTL19
GPR125
ZBTB49
ZNF721
C4orf34
TAPT1
FLJ39653
LCORL
ZNF718
CCDC96
BOD1L
DCAF4L1
CRIPAK
LOC285484
DOK7
FLJ35424
RNF212
LOC285540
LOC285547
LOC285548
FAM200B
C4orf10
NAT8L
LOC344967
C4orf44
FAM86EP
POLN
KCNIP4-IT1
C4orf52
BEND4
USP17L6P
USP17
HSP90AB2P
C4orf48
DTHD1
LOC401127
LOC402160
MIR218-1
LOC441009
ZNF876P
DEFB131
CLRN2
LOC650293
ZNF732
SCARNA22
MIR572
MIR573
MIR574
LOC728369
LOC728373
LOC728379
USP17L5
LOC728393
LOC728400
LOC728405
FLJ36777
RELL1
PSAPL1
MIR943
LOC100129917
LOC100129931
LOC100130872
LOC100133461
MIR548I2
TMED11P
MIR4274
MIR4275
MIR3138
SLIT2-IT1
LOC100505912
LOC100507266
MIR378D1
MIR548AJ2
MIR4802
MIR4800
MIR4801
MIR4798
HTT-AS1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q32.1.

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

Genes
ATIC
CHN1
CREB1
ERCC3
ACSL3
HOXD11
HOXD13
IDH1
NFE2L2
PAX3
PMS1
FEV
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
hsa-mir-26b
hsa-mir-548f-2
hsa-mir-1302-4
hsa-mir-2355
hsa-mir-3130-4
hsa-mir-3129
hsa-mir-1245
hsa-mir-561
hsa-mir-1258
hsa-mir-3128
hsa-mir-1246
hsa-mir-10b
hsa-mir-933
hsa-mir-128-1
hsa-mir-663b
AAMP
ACADL
ACVR1
ACVR2A
AGXT
ALPI
ALPP
ALPPL2
BIN1
AOX1
RND3
ATP5G3
KIF1A
BARD1
BCS1L
BMPR2
BOK
CACNB4
CASP8
CASP10
CCNT2
CD28
CHRNA1
CHRND
CHRNG
CLK1
COL3A1
COL4A3
COL4A4
COL5A2
COL6A3
CPS1
ATF2
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CTLA4
CYP27A1
DARS
DES
DLX1
DLX2
DYNC1I2
DPP4
DTYMK
EEF1B2
EPHA4
ERBB4
FAP
FN1
FRZB
GAD1
GALNT3
GBX2
GCG
MSTN
GLI2
GLS
GPC1
GPD2
GPR1
GPR17
GPR35
GPR39
GRB14
GYPC
HDLBP
HNMT
HOXD1
HOXD3
HOXD4
HOXD8
HOXD9
HOXD10
HOXD12
AGFG1
DNAJB2
HSPD1
HSPE1
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INHBB
INPP1
INPP5D
ITGA6
IRS1
ITGA4
ITGAV
ITGB6
KCNJ3
KCNJ13
KIF5C
LCT
LRP2
LY75
MAP2
MCM6
MGAT5
MYO1B
MYL1
MYO7B
NAB1
NCL
NEB
NDUFA10
NDUFB3
NDUFS1
SEPT2
NEU2
NEUROD1
NPPC
NR4A2
ORC2
ORC4
PDCD1
PDE1A
PDE6D
PDK1
SERPINE2
PLCL1
POLR2D
PPP1R7
PROC
PSMD1
PTH2R
PTMA
PTPRN
RALB
RBMS1
SNORD20
RPE
RPL37A
SAG
SCN1A
SCN2A
SCN3A
SCN7A
SCN9A
CCL20
SLC4A3
SLC11A1
SP3
SP100
SPP2
SSB
SSFA2
STAT1
STAT4
TFPI
TNFAIP6
TNP1
TNS1
TSN
TTN
TUBA4A
SUMO1
VIL1
WIPF1
WNT6
XRCC5
ZNF142
CXCR4
FZD5
SCG2
FZD7
SDPR
CUL3
PKP4
HAT1
DGKD
AGPS
PRKRA
STK16
SLC25A12
KLF7
ABCB11
B3GALT1
ADAM23
NRP2
CFLAR
PER2
CDK5R2
KYNU
NMI
RQCD1
LRRFIP1
STK17B
GPR55
TRIP12
GTF3C3
PPIG
HS6ST1
ECEL1
EIF4E2
CIR1
CYTIP
TTLL4
BZW1
HDAC4
ZEB2
FARP2
TLK1
CD302
TANK
FARSB
ABCB6
ARPC2
ARL4C
ABI2
DHRS9
CALCRL
PSMD14
STAM2
RAMP1
SPEG
LANCL1
NMUR1
KBTBD10
UBE2E3
STK25
MTX2
TBR1
MAP3K2
NCKAP1
COPS8
RAPGEF4
CAPN10
GALNT5
NXPH2
SP140
IKZF2
COBLL1
FASTKD2
PLA2R1
RAB3GAP1
PASK
UBXN4
ATG4B
SATB2
CLASP1
OBSL1
SF3B1
R3HDM1
DNPEP
TMEFF2
SH3BP4
KCNE4
NGEF
GCA
SNORD82
MOB4
PNKD
SNED1
GORASP2
SPATS2L
GIGYF2
EPC2
TRAF3IP1
ABCA12
ARL5A
HIBCH
PTPN18
SNORD51
CNPPD1
STK36
MMADHC
STK39
CPS1-IT1
METTL5
OLA1
C2orf27A
TFCP2L1
ICOS
GMPPA
BAZ2B
SLC40A1
SMARCAL1
ANO7
ARHGEF4
PDE11A
PRLH
THAP4
ANKMY1
GULP1
SCLY
NOP58
FKBP7
ASB1
CAB39
ZAK
LRP1B
PRKAG3
PPIL3
DNAJC10
ASNSD1
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
MFSD6
INO80D
PID1
PLEKHB2
ATG16L1
FIGN
ANKZF1
RIF1
USP40
WDR33
HJURP
STRADB
HES6
ACCN4
DOCK10
SMPD4
PRPF40A
IWS1
LIMS2
MREG
WDR12
MBD5
PECR
ARHGAP15
ZC3H15
CFC1
DNAH7
RPRM
UGGT1
C2orf83
MFF
CXCR7
RNPEPL1
SLC39A10
SLC4A10
CYP20A1
SPC25
ERMN
HECW2
MARCH4
WDFY1
NYAP2
ALS2
ZDBF2
USP37
CWC22
G6PC2
CTDSP1
MPP4
NIF3L1
PCGEM1
GAL3ST2
TMBIM1
IFIH1
OSGEPL1
RAB17
RNF25
COPS7B
MARCH7
OBFC2A
RAPH1
CDK15
TMEM237
NBEAL1
CFLAR-AS1
MRPL44
PLEKHA3
TRAK2
BOLL
TRPM8
ATG9A
MLPH
TMEM185B
FAM134A
GLB1L
C2orf47
SPAG16
CHPF
SAP130
SCRN3
FASTKD1
GTDC1
IQCA1
ALS2CR8
TTC21B
METTL8
NHEJ1
FAM124B
TM4SF20
CYBRD1
C2orf54
CSRNP3
PGAP1
DCAF17
TUBA4B
MZT2B
YSK4
ARMC9
COQ10B
EFHD1
SPHKAP
WNT10A
SLC19A3
THSD7B
KIAA1715
ILKAP
TMEM163
ITM2C
AMMECR1L
CDCA7
ZRANB3
RAB6C
WDR75
RHBDD1
C2orf88
ING5
CCDC115
MKI67IP
PLCD4
SFT2D3
LOC84931
MGC16025
TANC1
KCNH7
CCDC74A
LOC91149
SESTD1
CCDC74B
ANKRD44
ZNF804A
TTC30A
DAPL1
TMEM169
DNER
IMP4
MARS2
B3GNT7
SP140L
ORMDL1
TUBA3E
TUBA3D
STK11IP
FMNL2
GALNT13
OSBPL6
NOSTRIN
DIRC1
MOGAT1
LYPD1
AGAP1
TWIST2
PARD3B
NUP35
XIRP2
TYW5
DIS3L2
CNTNAP5
NEU4
RBM45
BBS5
C2orf77
ACMSD
ICA1L
FAM168B
RFTN2
AP1S3
SGPP2
ACVR1C
UBR3
KCTD18
ALS2CR12
SPATA3
LYPD6
LYPD6B
TMEM198
ZFAND2B
CPO
MDH1B
FBXO36
MTERFD2
CCDC148
MYO3B
UBE2F
DUSP19
LOC150527
FLJ32063
OTOS
MYEOV2
OR6B3
ANKAR
TTC30B
LOC150776
WTH3DI
FAM117B
LOC150935
PKI55
C2orf67
ZSWIM2
ZNF385B
LOC151171
LOC151174
ARL6IP6
METTL21A
CCNYL1
KLHL23
PPP1R1C
SGOL2
ALS2CR11
SLC38A11
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDSUB1
UPP2
GPR155
WDR69
C2orf57
FAM171B
PIKFYVE
LOC200726
TIGD1
LOC200772
FAM123C
C2orf69
HNRNPA3
CERS6
METAP1D
LOC254128
CCDC108
C2orf72
CCDC150
CCDC141
LOC285084
CXXC11
LOC285103
FAM126B
UNC80
RUFY4
DUSP28
SPOPL
MLK7-AS1
CYP27C1
ESPNL
NCKAP5
EVX2
AOX2P
GPR148
ECEL1P2
FONG
LOC348761
RBM43
LOC375295
CERKL
C2orf62
RBM44
AQP12A
KLHL30
LOC389033
LOC389043
SP5
PLEKHM3
C2orf80
RESP18
C2orf82
OR6B2
DYTN
LOC401010
DKFZp686O1327
LOC401022
FSIP2
C2orf66
ASB18
FLJ43879
VWC2L
MIR10B
MIR128-1
MIR149
MIR153-1
MIR26B
C2orf27B
DNAJB3
LOC440905
LOC440910
POTEKP
LOC440925
POTEE
PHOSPHO2
MIR375
DFNB59
LOC554201
ANKRD30BL
SNORA41
LOC643387
PRR21
LOC646324
LOC646736
LOC646743
PRSS56
LOC647012
CFC1B
AQP12B
MZT2A
SNORA75
SCARNA6
SCARNA5
SNORD11
SNORD70
MIR561
D2HGDH
LOC728323
POTEF
PABPC1P2
DIRC3
SNORD11B
MIR933
LOC100129175
LOC100129961
PP14571
LOC100130451
LOC100130452
LOC100130691
TMEM194B
LOC100131320
SP9
CYP4F30P
LOC100144595
RNU4ATAC
LOC100216479
LOC100286922
MIR1471
MIR1246
MIR548N
MIR1258
MIR1245A
MIR1244-1
ZEB2-AS1
MIR548F2
MIR663B
LOC100329109
SNORA70F
BOK-AS1
MIR3128
MIR1244-3
MIR1244-2
MIR3129
MIR3131
MIR4268
MIR3130-1
MIR3130-2
MIR2355
MIR3132
MIR4269
MIR3606
MIR3679
LOC100505695
LOC100506124
LOC100506134
LOC100506783
LOC100506866
LOC100507140
LOC100507443
LOC100507600
LY75-CD302
PHOSPHO2-KLHL23
HSPE1-MOB4
UBE2F-SCLY
MIR4783
MIR4439
MIR4437
MIR4776-1
MIR4777
MIR1245B
MIR4774
MIR2467
MIR4775
MIR4785
MIR4784
MIR4773-1
MIR4444-1
MIR4440
MIR4786
MIR4773-2
MIR4776-2
MIR4441
LOC100861402
Genes in Wide Peak

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

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

Genes
GATA3
MLLT10
hsa-mir-603
hsa-mir-1915
hsa-mir-511-2
hsa-mir-511-1
hsa-mir-1265
hsa-mir-548q
hsa-mir-3155
ADARB2
ATP5C1
BMI1
CACNB2
CALML3
AKR1C4
KLF6
AKR1C1
AKR1C2
TRDMT1
GDI2
IDI1
IL2RA
IL15RA
ITIH2
MRC1
PFKFB3
PFKP
PHYH
PIP4K2A
PRKCQ
RSU1
VIM
STAM
CUBN
ITGA8
PRPF18
AKR1C3
CDC123
PTPLA
PTER
NMT2
SPAG6
USP6NL
OPTN
NET1
NEBL
PITRM1
RPP38
CELF2
ZMYND11
NUDT5
WDR37
MSRB2
SEPHS1
KIN
DIP2C
LARP4B
COMMD3
GTPBP4
UPF2
HSPA14
CALML5
ANKRD16
FAM208B
SEC61A2
OLAH
MCM10
DHTKD1
FRMD4A
IDI2-AS1
KIAA1217
PRTFDC1
CAMK1D
GPR158
ARHGAP21
SFMBT2
DNAJC1
DCLRE1C
SUV39H2
ECHDC3
ASB13
TUBAL3
THNSL1
FAM188A
ITIH5
AKR1E2
FAM107B
CCDC3
TAF3
FBXO18
PLXDC2
RBM17
IDI2
UCN3
SFTA1P
ENKUR
ARMC3
LOC219731
OTUD1
UCMA
C10orf111
FAM171A1
SLC39A12
NSUN6
ARL5B
BEND7
LOC254312
C10orf47
PTF1A
C10orf67
LOC282980
LOC283070
LOC338588
ST8SIA6
AKR1CL1
EBLN1
TUBB8
C10orf113
C10orf140
tAKR
C1QL3
LINC00200
LOC399708
LOC399715
FLJ45983
C10orf114
ACBD7
C10orf108
LOC439949
LOC439950
CDNF
MIR511-1
MIR511-2
ADARB2-AS1
MEIG1
TMEM236
MIR603
LOC100128098
LOC100128511
LOC100128811
LOC100129213
LOC100130992
PRINS
LOC100192204
LOC100216001
MIR1265
MIR1915
MIR3155A
LOC100499489
LOC100507034
LOC100507127
COMMD3-BMI1
MIR4480
MIR4675
MIR3155B
Genes in Wide Peak

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

Table S62.  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
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
hsa-mir-186
hsa-mir-1262
hsa-mir-3117
hsa-mir-101-1
hsa-mir-3116-2
ABCA4
ACADM
ADORA3
AGL
AK4
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
BRDT
C8A
C8B
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CRYZ
CSF1
CTBS
CTH
CYP2J2
DAB1
DBT
GADD45A
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
FCGR1A
FCGR1B
FMO5
GBP1
GBP2
GBP3
GFI1
GJA5
GJA8
GCLM
GNAI3
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
HMGCS2
HSD3B1
HSD3B2
IGSF3
CYR61
IL12RB2
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
LEPR
TACSTD2
MOV10
MSH4
NFIA
NGF
NHLH2
ROR1
OVGP1
PDE4B
PDZK1
PGM1
PIN1P1
PRKAA2
PRKAB2
PRKACB
PKN2
PSMA5
PTGER3
PTGFR
PTGFRN
ABCD3
RABGGTB
RAP1A
SNORD21
RPE65
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TGFBR3
TSHB
USP1
VCAM1
WNT2B
BSND
CSDE1
EVI5
CDC7
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
BCAR3
TTF2
ITGA10
LMO4
CDC14A
PPAP2B
RTCD1
FPGT
PEX11B
FUBP1
DIRAS3
SLC16A4
SRSF11
CD101
SEP15
ZRANB2
ARHGAP29
SEC22B
CHD1L
CLCA3P
CLCA2
HS2ST1
DNAJC6
LRIG2
LPPR4
SV2A
RBM8A
INSL5
PIGK
TSPAN2
INADL
BCAS2
WARS2
CEPT1
PIAS3
VAV3
HBXIP
IFI44
POLR3C
TXNIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
IFI44L
DNAJB4
ADAM30
CD160
GLMN
HHLA3
DDX20
CLCA4
MTF2
NTNG1
WDR47
USP33
CLCC1
SLC35D1
LPHN2
KIAA1107
USP24
ITGB3BP
SLC35A3
LRRC8B
LPAR3
DDAH1
NBPF14
RWDD3
ZZZ3
SERBP1
PTPN22
PHGDH
AK5
SNORA66
SNORD45B
SNORD45A
FOXD3
CHIA
RNF115
ANGPTL3
GPSM2
ALG6
SLC25A24
DNTTIP2
TMED5
BOLA1
TNNI3K
SH3GLB1
HAO2
ACP6
HOOK1
SNX7
GPR89B
DPH5
GPR88
CCDC76
L1TD1
RSBN1
ZNHIT6
LEPROT
GIPC2
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
RAVER2
FGGY
MCOLN3
SLC22A15
RNPC3
LRRC40
DEPDC1
LRIF1
CTTNBP2NL
FAM212B
GNG12
CCBL2
TMEM167B
OLFML3
FAM91A2
AMIGO1
ODF2L
KIAA1324
LRRC7
CACHD1
MIER1
PTBP2
DNASE2B
ELTD1
HIAT1
DCLRE1B
WDR77
DLEU2L
EPS8L3
VTCN1
TTLL7
WDR78
RPAP2
DENND2D
WLS
RPF1
SIKE1
TRIM45
ANKRD13C
VANGL1
ST6GALNAC5
GPR61
TM2D1
REG4
SYDE2
ZNF644
LRRC8C
SGIP1
POLR3GL
PROK1
EFCAB7
PSRC1
ATP1A1OS
ATG4C
FAM40A
DOCK7
ZNF697
NEXN
DNAJA1P5
HENMT1
MYSM1
GNRHR2
OMA1
GBP4
GBP5
SSX2IP
OLFM3
WDR63
MAB21L3
HIST2H3C
SLC44A3
ATXN7L2
C1orf194
ASB17
TYW3
C1orf173
LRRIQ3
LRRC39
C1orf87
LIX1L
HSD3BP4
DRAM2
C1orf88
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
UBE2U
HFE2
ANKRD35
SLC30A7
MGC27382
IL23R
RP11-165H20.1
DENND2C
GBP6
LPPR5
FNDC7
KANK4
SASS6
PPIAL4A
HFM1
UBL4B
PDIA3P
ALG14
LINC00466
C1orf168
TMEM61
NBPF11
NUDT17
TCTEX1D1
SPAG17
HIPK1
SLC44A5
AKR7A2P1
EPHX4
AKNAD1
MCOLN2
COL24A1
PCSK9
ST6GALNAC3
NEGR1
MAGI3
FAM19A3
NBPF15
FAM102B
SYPL2
CYB561D1
ANKRD34A
ZNF326
BTBD8
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BC
HIST2H2BA
LOC339524
CCDC18
MYBPHL
BARHL2
HSP90B3P
NBPF7
FAM73A
LOC375010
GBP7
C1orf146
FAM69A
SLC6A17
NOTCH2NL
FLJ39739
LOC388692
UOX
FRRS1
C1orf141
GBP1P1
FLJ27354
MIR137HG
NBPF9
MIR101-1
MIR137
MIR186
MIR197
LHX8
C1orf180
FLJ31662
LOC440600
BCL2L15
HIST2H2BF
PGCP1
GEMIN8P4
RBMXL1
HIST2H4B
SRG7
CYMP
LOC643441
LOC644242
PPIAL4G
PPIAL4D
LOC645166
LOC646626
EMBP1
SRGAP2P2
LOC648740
NBPF6
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
SCARNA2
SNORD45C
MIR548D1
MIR553
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
HSD52
LOC729970
LOC729987
PPIAL4E
PFN1P2
MIR942
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129269
LOC100129620
LOC100130000
LOC100131060
LOC100131564
NBPF10
FCGR1C
ZRANB2-AS1
LOC100286793
LOC100287722
LOC100289178
LOC100289211
MIR320B1
MIR1262
MIR3117
MIR4256
MIR3671
MIR548AA1
LOC100505768
LOC100506343
LOC100507634
FPGT-TNNI3K
TMEM56-RWDD3
MIR4422
MIR4794
MIR4711
MIR2682
MIR4423
NEGR1-IT1
ZRANB2-AS2
Genes in Wide Peak

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

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

Genes
LCP1
RB1
LHFP
TTL
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
ATP7B
RCBTB2
CPB2
ELF1
ESD
FOXO1
MLNR
GTF2F2
GUCY1B2
HTR2A
KPNA3
MAB21L1
SMAD9
NEK3
PCDH8
PCDH9
RFXAP
ATXN8OS
TPT1
TRPC4
TNFSF11
SUCLA2
DLEU2
TSC22D1
CCNA1
DCLK1
ITM2B
MTRF1
UTP14C
LPAR6
SLC25A15
TRIM13
MRPS31
DLEU1
OLFM4
POSTN
SUGT1
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
KIAA0564
ZC3H13
SPG20
LRCH1
INTS6
CKAP2
NUFIP1
NBEA
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
PHF11
UFM1
SOHLH2
ENOX1
RCBTB1
NUDT15
KIAA1704
FAM48A
THSD1
CYSLTR2
SPRYD7
COG6
KLHL1
PCDH20
NAA16
RNASEH2B
DHRS12
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KBTBD7
EBPL
KBTBD6
EPSTI1
ARL11
WDFY2
LINC00284
CSNK1A1L
PRR20A
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
DGKH
CCDC122
STOML3
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
SLC25A30
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
LINC00550
FREM2
NEK5
THSD1P1
KCTD4
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
MIR15A
MIR16-1
ALG11
TSC22D1-AS1
SERPINE3
SNORA31
MIR621
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
TPT1-AS1
MIR1297
MIR548F5
MIR759
MIR320D1
MIR4305
MIR3169
MIR3613
OR7E37P
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
MIR4703
LOC100616668
Genes in Wide Peak

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

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

Genes
EML4
ZFP36L2
PPM1B
SIX3
SLC3A1
COX7A2L
PREPL
LRPPRC
SIX2
HAAO
DYNC2LI1
SRBD1
MTA3
THADA
ABCG5
ABCG8
CAMKMT
PKDCC
PLEKHH2
OXER1
KCNG3
LOC388942
LOC400950
UNQ6975
LOC728819
LOC100129726
MIR548AD
Genes in Wide Peak

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

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

Genes
GNAS
TOP1
MAFB
SS18L1
ASXL1
hsa-mir-647
hsa-mir-4326
hsa-mir-124-3
hsa-mir-133a-2
hsa-mir-3195
hsa-mir-1257
hsa-mir-646
hsa-mir-298
hsa-mir-4325
hsa-mir-1302-5
hsa-mir-1259
hsa-mir-1289-1
hsa-mir-499
hsa-mir-644
hsa-mir-1825
hsa-mir-3193
hsa-mir-663
hsa-mir-3192
hsa-mir-103-2-as
hsa-mir-1292
hsa-mir-3194
ADA
ADRA1D
JAG1
AHCY
ASIP
ATP5E
AVP
BCL2L1
BFSP1
BMP2
BMP7
BPI
ENTPD6
CD40
CDC25B
CDH4
CEBPB
CENPB
CHGB
CHRNA4
COL9A3
CSE1L
CSNK2A1
CST1
CST2
CST3
CST4
CST5
CSTF1
CTSZ
CYP24A1
DNMT3B
E2F1
EDN3
EEF1A2
EPB41L1
EYA2
FKBP1A
FOXS1
GGT7
GHRH
GNRH2
NPBWR2
GSS
HCK
FOXA2
HNF4A
ID1
IDH3B
INSM1
EIF6
ITPA
KCNB1
KCNG1
KCNQ2
KCNS1
LAMA5
LBP
MC3R
MMP9
MYBL2
MYT1
NFATC2
NKX2-2
NNAT
NTSR1
OPRL1
OXT
PAX1
PCK1
PCNA
PCSK2
PDYN
PFDN4
PI3
PLAGL2
PLCB4
PLCG1
PLTP
CTSA
PPP1R3D
PRNP
PSMA7
PTGIS
PTK6
PTPN1
PTPRA
PYGB
RBL1
RPN2
RPS21
RRBP1
SDC4
SEMG1
SEMG2
SRSF6
SLPI
SIGLEC1
SNAI1
SNAP25
SNRPB
SNRPB2
SNTA1
SOX12
SPAG4
SRC
SRMS
SSTR4
STAU1
STK4
AURKA
TAF4
TCEA2
TCF15
TFAP2C
TGM2
TGM3
THBD
TNNC2
TPD52L2
UBE2V1
YWHAB
MKRN7P
ZNF133
ZNF217
MKKS
GDF5
NCOA3
ATRN
RAE1
CST7
BCAS1
STX16
CDS2
TNFRSF6B
MATN4
DPM1
WISP2
EIF2S2
CPNE1
NFS1
CBFA2T2
VAPB
B4GALT5
KIF3B
PSMF1
RBM39
TTI1
SNPH
ProSAPiP1
RASSF2
TM9SF4
SPATA2
GINS1
OSBPL2
SLC23A2
ACOT8
CST8
ATP9A
SGK2
RBM12
ARFRP1
RGS19
SIRPB1
SYCP2
MYL9
WFDC2
SEC23B
NOP56
PROCR
ARFGEF2
RBCK1
POLR3F
TCFL5
RBBP9
SPINT3
MMP24
BLCAP
TOMM34
SERINC3
DSTN
ADRM1
OGFR
UBE2C
DIDO1
PTPRT
PKIG
CEP250
RNF24
HRH3
PXMP4
RBPJL
XRN2
DLGAP4
UBOX5
BTBD3
RALY
CD93
MAPRE1
TPX2
NINL
ZHX3
NCOA6
PLCB1
SLC9A8
ADNP
POFUT1
ZMYND8
SPO11
PRND
FLRT3
LAMP5
PRPF6
SPEF1
SAMHD1
C20orf194
C20orf4
L3MBTL1
PPP1R16B
C20orf26
ABHD12
TRPC4AP
ZNF337
GTPBP5
GMEB2
SNORD12C
SNORA71B
SNORA71A
SNORD57
SNORD56
SDCBP2
SNX5
TP53TG5
MOCS3
SLCO4A1
REM1
C20orf30
HSPC072
NXT1
VSX1
STMN3
SLC35C2
SLMO2
IFT52
NAA20
PHF20
SCAND1
BPIFA1
CRNKL1
ANGPT4
TH1L
C20orf43
C20orf111
ESF1
PIGT
TRMT6
ERGIC3
CDK5RAP1
RTEL1
SOX18
HAO1
RIN2
SMOX
CRLS1
YTHDF1
LIME1
UCKL1
C20orf27
C20orf11
DZANK1
UQCC
PCMTD2
C20orf20
SPTLC3
C20orf29
TMEM74B
PPP4R1L
SIRPG
RBM38
FERMT1
KIF16B
TASP1
BCAS4
DDX27
ZNF334
ZFP64
ARFGAP1
EDEM2
DOK5
PLK1S1
DBNDD2
ACSS2
RNF114
SULF2
NSFL1C
C20orf24
TMX4
CTNNBL1
GPCPD1
CPXM1
SLC2A4RG
OTOR
PMEPA1
CASS4
SPINLW1
C20orf3
PAK7
RALGAPB
JPH2
SALL4
ZNFX1
RALGAPA2
CSRP2BP
RAB22A
SLC24A3
NDRG3
SLC12A5
ZNF512B
MAVS
PREX1
EBF4
COL20A1
MYH7B
NCOA5
TRIB3
TP53INP2
RPRD1B
OVOL2
TGIF2
CDH26
FASTKD5
KCNK15
DHX35
MANBAL
NAPB
SLC17A9
ELMO2
ZNF335
ANKRD5
LOC63930
PCIF1
FAM217B
NECAB3
GFRA4
CDH22
GZF1
VPS16
FAM113A
SLC13A3
LPIN3
MRPS26
DDRGK1
GDAP1L1
LOC79015
C20orf195
C20orf7
PPDPF
ZNF343
TTPAL
BIRC7
NPEPL1
ACTR5
SYNDIG1
DSN1
NRSN2
PANK2
FER1L4
DNAJC5
ADAM33
PABPC1L
BPIFB2
SEL1L2
TUBB1
ZBP1
SLC2A10
HM13
PDRG1
FAM83D
DEFB126
CABLES2
FAM110A
DYNLRB1
ITCH
SLC4A11
SLA2
CHD6
MCM8
ACSS1
MAP1LC3A
PARD6B
ZGPAT
COX4I2
ZNF341
TOX2
ZCCHC3
MYLK2
PRIC285
KIAA1755
SCRT2
EMILIN3
SYS1
WFDC8
SNX21
ZSWIM1
GGTLC1
C20orf72
DTD1
BPIFB1
TP53RK
C20orf54
DNTTIP1
FAM210B
PHACTR3
HSPA12B
DEFB118
TMC2
BHLHE23
NKAIN4
VSTM2L
SNHG11
FITM2
WFDC12
SPATA25
C20orf123
TSHZ2
C20orf85
ZNF831
TBC1D20
SIRPD
C20orf141
PROKR2
C20orf94
CSTL1
CST9L
CST9
C20orf166
DUSP15
TSPY26P
BPIFB6
BPIFA3
C20orf144
CHMP4B
PIGU
HMGB3P1
FAM83C
GATA5
MLLT10P1
SLC32A1
C20orf96
BPIFA2
ZBTB46
WFDC3
GCNT7
C20orf112
CBLN4
CTCFL
C20orf132
SAMD10
ABHD16B
C20orf160
KIAA0889
C20orf118
RIMS4
SUN5
MACROD2
SRXN1
ROMO1
NEURL2
LINC00261
ZSWIM3
WFDC10A
BANF2
NANP
LINC00266-1
DEFB127
C20orf79
ISM1
WFDC6
C20orf173
LINC00028
FAM65C
CST11
DEFB129
SIRPA
C20orf151
C20orf152
STK35
R3HDML
ADIG
GTSF1L
WFDC5
LOC149773
GNAS-AS1
PRNT
LOC149837
C20orf196
NCOR1P1
LOC149950
COMMD7
BPIFB4
LSM14B
WFDC13
APCDD1L
LRRN4
CSTT
TTLL9
ACTL10
C20orf201
FAM209A
LOC200261
DEFB115
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
DEFB125
DEFB128
C20orf166-AS1
WFDC11
WFDC9
WFDC10B
LINC00176
LINC00494
LOC284751
C20orf197
LOC284757
SIRPB2
LOC284788
LOC284798
FAM182A
LOC284801
FRG1B
C20orf203
BPIFA4P
LOC339568
LOC339593
ARHGAP40
RSPO4
TGM6
XKR7
BPIFB3
TMEM189
TMEM189-UBE2V1
LINC00493
LOC388796
FAM209B
SPINT4
SUMO1P1
DEFB132
C20orf202
FLJ33581
MIR103A2
MIR1-1
MIR124-3
MIR133A2
MIR296
DZANK1-AS1
ZNFX1-AS1
MIR499A
RAD21L1
LOC643406
NKX2-4
LOC647979
SNORA39
SNORA51
SNORA60
SNORA71C
SNORA71D
SNORD12
SNORD17
SNORD86
SNORD110
MIR644A
MIR645
MIR647
MIR663A
LOC728228
FAM182B
SYS1-DBNDD2
HAR1A
HAR1B
PSIMCT-1
SNORD119
UCKL1-AS1
SNORD12B
MIR298
MIR941-1
MIR941-4
MIR941-2
MIR941-3
LOC100127888
LOC100128496
LOC100130264
ZNF663
LOC100131208
LOC100131496
DPH3P1
LOC100134015
LOC100134868
LINC00029
LOC100144597
FLJ16779
LOC100270679
LOC100270804
LOC100287792
TMEM239
LOC100289473
MIR1914
MIR1292
MIR1257
MIR103B2
PCNA-AS1
PET117
MACROD2-AS1
MIR3192
MIR4325
MIR3194
MIR3193
MIR4326
MIR3196
MTRNR2L3
MIR3646
MIR3616
LOC100505536
LOC100505783
LOC100505815
LOC100505826
LOC100506384
LOC100507495
LOC100507629
SPINLW1-WFDC6
TGIF2-C20ORF24
FKBP1A-SDCBP2
RTEL1-TNFRSF6B
SLMO2-ATP5E
STX16-NPEPL1
MIR499B
MIR4756
MIR4758
MIR4532
MIR4533
MIR4755
MIR5095
LOC100652730
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 2121 0.07 -2.75 1 0.25 9.01 0
1q 1955 0.18 3.39 0.00176 0.17 2.73 0.0107
2p 924 0.18 -1.29 1 0.02 -8.63 1
2q 1556 0.17 0.805 0.569 0.02 -7.18 1
3p 1062 0.11 -4.08 1 0.14 -2.78 1
3q 1139 0.15 -1.98 1 0.10 -4.41 1
4p 489 0.03 -8.39 1 0.31 3.89 0.000201
4q 1049 0.04 -6.8 1 0.29 5.08 8.19e-07
5p 270 0.15 -4.24 1 0.16 -3.87 1
5q 1427 0.09 -3.66 1 0.20 2.05 0.0624
6p 1173 0.20 0.795 0.569 0.10 -4.18 1
6q 839 0.18 -1.24 1 0.13 -3.62 1
7p 641 0.54 16.1 0 0.01 -7.08 1
7q 1277 0.49 17.4 0 0.02 -6.21 1
8p 580 0.35 4.72 6.73e-06 0.49 11.8 0
8q 859 0.50 14.6 0 0.18 -1.16 1
9p 422 0.19 -2.2 1 0.15 -4.03 1
9q 1113 0.17 -1.07 1 0.14 -2.27 1
10p 409 0.08 -7.32 1 0.17 -3.23 1
10q 1268 0.05 -6.53 1 0.17 -0.412 1
11p 862 0.13 -3.83 1 0.13 -3.52 1
11q 1515 0.13 -1.75 1 0.16 0.152 1
12p 575 0.23 0.0428 1 0.13 -4.11 1
12q 1447 0.21 2.56 0.0208 0.14 -1.16 1
13q 654 0.59 18.1 0 0.07 -5.04 1
14q 1341 0.11 -2.74 1 0.33 8.58 0
15q 1355 0.04 -5.8 1 0.35 10 0
16p 872 0.25 2.21 0.0497 0.10 -4.87 1
16q 702 0.24 1.14 0.391 0.09 -5.65 1
17p 683 0.09 -4.55 1 0.57 17.3 0
17q 1592 0.21 2.88 0.00871 0.18 1.44 0.198
18p 143 0.10 -5.12 1 0.59 15.7 0
18q 446 0.07 -5.22 1 0.62 18.5 0
19p 995 0.16 -1.87 1 0.12 -3.47 1
19q 1709 0.18 2.11 0.0584 0.11 -1.75 1
20p 355 0.57 14.9 0 0.29 1.66 0.139
20q 753 0.71 24.5 0 0.15 -1.79 1
21q 509 0.07 -6.86 1 0.29 2.75 0.0107
22q 921 0.04 -6.92 1 0.33 6.66 6.83e-11
Xq 1312 0.17 -0.0161 1 0.15 -1.15 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/9824618/GDAC_MergeDataFiles_9826162/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_with_miR_20120227.mat

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

  • Amplification Threshold = 0.1

  • Deletion Threshold = 0.1

  • Cap Values = 1.5

  • Broad Length Cutoff = 0.7

  • Remove X-Chromosome = 0

  • Confidence Level = 0.99

  • Join Segment Size = 4

  • Arm Level Peel Off = 1

  • Maximum Sample Segments = 2000

  • Gene GISTIC = 1

Table 4.  Get Full Table First 10 out of 438 Input Tumor Samples.

Tumor Sample Names
TCGA-3L-AA1B-01A-11D-A36W-01
TCGA-4N-A93T-01A-11D-A36W-01
TCGA-A6-2671-01A-01D-1549-01
TCGA-A6-2672-01A-01D-1549-01
TCGA-A6-2674-01A-02D-1549-01
TCGA-A6-2675-01A-02D-1717-01
TCGA-A6-2676-01A-01D-1549-01
TCGA-A6-2677-01A-01D-1549-01
TCGA-A6-2678-01A-01D-1549-01
TCGA-A6-2679-01A-02D-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)
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