SNP6 Copy number analysis (GISTIC2)
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
04 October 2018  |  None
Maintainer Information
Maintained by Broad Institute GDAC (Broad Institute of MIT & Harvard)
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 2.0.23.

Summary

There were 100 tumor samples used in this analysis: 41 significant arm-level results, 48 significant focal amplifications, and 63 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 - 48 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
17q12 8.1508e-15 2.8574e-14 chr17:37791859-37902258 9
16p11.2 6.6195e-12 6.6195e-12 chr16:28617090-28631468 1
12p13.33 2.5885e-09 2.5885e-09 chr12:1-905787 10
1q32.2 1.7635e-11 9.7134e-07 chr1:207700087-207737384 1
9p24.3 1.2893e-06 1.2893e-06 chr9:1-30280 0 [FAM138C]
7q22.1 1.8035e-07 1.3037e-06 chr7:101961755-102006564 2
2q13 2.9013e-06 7.2168e-06 chr2:113955323-114251318 3
15q26.3 3.5006e-05 7.4605e-05 chr15:102512727-102531392 2
1q22 4.9282e-05 8.7353e-05 chr1:156013717-156139761 6
Xp11.23 4.9282e-05 0.00023163 chrX:49242802-49358887 9
6p21.32 0.00036106 0.00036106 chr6:33084735-33148997 2
8q22.3 0.00039847 0.00039847 chr8:100844547-103674265 30
22q13.2 0.00052554 0.00052554 chr22:42523399-42537405 2
7q11.23 0.00023163 0.00064456 chr7:74925008-74981239 0 [STAG3L1]
20q13.33 0.00077584 0.00077584 chr20:60639506-60907799 10
Xq24 7.7065e-05 0.0008558 chrX:120012654-120117755 12
2q11.1 0.00046813 0.0013565 chr2:96562948-96587592 1
19q13.2 0.0003196 0.0014333 chr19:40276338-40408849 4
Xq28 0.00048683 0.001886 chrX:155250626-155270560 1
3p21.31 0.010779 0.010779 chr3:47030144-47050177 1
12q13.2 0.00094188 0.010779 chr12:56522092-56592222 5
11q13.3 0.0011142 0.011493 chr11:69062821-69597209 5
11p11.2 0.0129 0.013927 chr11:46690343-46760718 4
19q12 3.624e-05 0.015078 chr19:30294167-30469143 2
2p23.3 0.01731 0.01731 chr2:26676187-26803538 3
1p36.33 0.013927 0.018012 chr1:1-3311498 77
Xp11.23 0.0019388 0.022321 chrX:49211696-49294531 5
14q24.2 0.024262 0.024262 chr14:73706405-73732216 1
7p13 0.025266 0.025266 chr7:43992726-44084464 6
15q24.2 0.015323 0.034079 chr15:75580548-75586601 2
19p13.11 0.0046432 0.039468 chr19:17442103-17461638 2
13q12.11 0.043708 0.043708 chr13:21720943-21750617 2
3q26.2 0.00088284 0.045673 chr3:168269641-169099311 3
1p36.13 0.050237 0.057693 chr1:16343718-16543103 7
3q27.1 0.010779 0.065532 chr3:184032255-184542419 11
4p16.3 0.075458 0.075458 chr4:2507141-3048602 8
18p11.31 0.091325 0.091325 chr18:2904162-3269919 6
9q34.3 0.095795 0.095795 chr9:140917839-141213431 3
10q23.2 0.072018 0.095795 chr10:86227539-88811110 17
11p15.2 0.062011 0.095795 chr11:13743226-15267587 13
17q24.1 0.016902 0.10788 chr17:62882142-62888733 1
11q13.2 0.0010706 0.11254 chr11:67017557-67783915 33
16q22.2 0.13744 0.13744 chr16:72089951-72094788 3
6q25.1 0.15679 0.15679 chr6:151805727-152211242 2
12q24.31 0.1168 0.16935 chr12:124487658-125474586 8
10q26.13 0.031202 0.17934 chr10:122666238-123503374 4
5q35.2 0.21014 0.21014 chr5:176483229-176563110 3
19p13.2 0.0046432 0.21114 chr19:10958276-11412196 13
Genes in Wide Peak

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

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

Genes
ERBB2
STARD3
PPP1R1B
GRB7
MIEN1
PNMT
PGAP3
TCAP
MIR4728
Genes in Wide Peak

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

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

Genes
SULT1A1
Genes in Wide Peak

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

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

Genes
KDM5A
SLC6A13
WNK1
SLC6A12
IQSEC3
CCDC77
B4GALNT3
NINJ2
FAM138D
RNU4ATAC16P
Genes in Wide Peak

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

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

Genes
CR1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q22.1.

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

Genes
PRKRIP1
SH2B2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2q13.

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

Genes
PAX8
PSD4
CBWD2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.3.

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

Genes
WASH3P
DDX11L9
Genes in Wide Peak

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

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

Genes
LAMTOR2
RAB25
LMNA
UBQLN4
SEMA4A
MEX3A
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp11.23.

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

Genes
GAGE2A
GAGE12G
GAGE12E
GAGE12H
GAGE12D
GAGE2B
GAGE12F
GAGE12B
GAGE12C
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.32.

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

Genes
COL11A2
HCG24
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q22.3.

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

Genes
COX6C
RNF19A
RRM2B
PABPC1
GRHL2
SPAG1
NCALD
UBR5
ZNF706
VPS13B
RGS22
POLR2K
ODF1
KLF10
FBXO43
YWHAZ
SNX31
ANKRD46
RN7SKP249
SNORD77|ENSG00000212414.1
RNU6ATAC8P
RNU6ATAC41P
MIR1273A
NACAP1
snoU13|ENSG00000238372.1
snoU13|ENSG00000238533.1
RN7SL563P
RN7SL685P
MIR4471
MIR5680
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 22q13.2.

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

Genes
CYP2D6
CYP2D7P1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.33.

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

Genes
SS18L1
HRH3
MTG2
PSMA7
TAF4
LAMA5
OSBPL2
ADRM1
LSM14B
MIR4758
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq24.

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

Genes
CT47A10
CT47A6
CT47A9
CT47A12
CT47A11
CT47A7
CT47A8
CT47A4
CT47A3
CT47A1
CT47A5
CT47A2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2q11.1.

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

Genes
ANKRD36C
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.2.

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

Genes
FCGBP
FBL
DYRK1B
LEUTX
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xq28.

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

Genes
WASH6P|ENSG00000182484.10
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3p21.31.

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

Genes
NBEAL2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q13.2.

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

Genes
MYL6
SMARCC2
ESYT1
MYL6B
RN7SL770P
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.3.

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

Genes
CCND1
FGF4
ORAOV1
FGF19
MYEOV
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p11.2.

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

Genes
ZNF408
ARHGAP1
ATG13
F2
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q12.

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

Genes
CCNE1
URI1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p23.3.

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

Genes
OTOF
DRC1
C2orf70
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p36.33.

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

Genes
PRDM16
TNFRSF14
CDK11A
NADK
PRKCZ
GNB1
SDF4
DVL1
MORN1
CPSF3L
ACAP3
C1orf159
MMEL1
C1orf222
PLCH2
FAM213B
PANK4
PEX10
RER1
SKI
ATAD3B
SSU72
UBE2J2
TTLL10
SCNN1D
MXRA8
C1orf86
ACTRT2
CALML6
TAS1R3
PUSL1
AURKAIP1
B3GALT6
LINC00982
FAM87B
TMEM52
VWA1
FAM132A
OR4F16
OR4F5
TNFRSF4
TNFRSF18
PLEKHN1
ISG15
SAMD11
C1orf170
GABRD
KLHL17
AGRN
HES4
NOC2L
SLC35E2B
MMP23B
MIB2
ATAD3A
HES5
MIR429
TMEM240
TMEM88B
MIR200A
MIR200B
SLC35E2
TTC34
ATAD3C
CCNL2
DDX11L1
GLTPD1
LINC00115
C1orf233
FAM41C
ANKRD65
OR4F29
RNF223
FAM138A
MRPL20
CDK11B
RN7SL657P
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp11.23.

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

Genes
GAGE2B
GAGE2C
GAGE12B
GAGE2D
GAGE12I
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q24.2.

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

Genes
PAPLN
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p13.

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

Genes
UBE2D4
SPDYE1
DBNL
POLR2J4
RASA4CP
LINC00957
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q24.2.

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

Genes
GOLGA6D
RN7SL327P
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19p13.11.

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

Genes
ANO8
GTPBP3
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q12.11.

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

Genes
SAP18
SKA3
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.2.

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

Genes
MECOM
EGFEM1P
MIR551B
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p36.13.

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

Genes
EPHA2
ARHGEF19
HSPB7
CLCNKB
FAM131C
CLCNKA
ANO7P1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q27.1.

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

Genes
THPO
CHRD
CLCN2
EIF4G1
EIF2B5
VPS8
POLR2H
FAM131A
MAGEF1
EPHB3
SNORD66|ENSG00000212158.1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4p16.3.

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

Genes
RNF4
SH3BP2
NOP14
ADD1
MFSD10
FAM193A
GRK4
TNIP2
Genes in Wide Peak

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

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

Genes
LPIN2
MYOM1
MYL12A
MYL12B
EMILIN2
SNORA70|ENSG00000252258.1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9q34.3.

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

Genes
CACNA1B
TUBBP5
FAM157B
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q23.2.

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

Genes
BMPR1A
WAPAL
CCSER2
LDB3
OPN4
ADIRF
GLUD1
AGAP11
SNCG
MMRN2
GRID1
FAM25A
MIR346
RNA5SP322
U3|ENSG00000252189.1
RN7SKP238
RN7SKP84
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p15.2.

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

Genes
CALCA
COPB1
PSMA1
RRAS2
SPON1
PDE3B
CALCB
CYP2R1
INSC
FAR1
RNA5SP331
RNA5SP332
PSMA1
Genes in Wide Peak

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

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

Genes
LRRC37A3
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.2.

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

Genes
ALDH3B1
GSTP1
UNC93B1
PITPNM1
AIP
ACY3
ALDH3B2
FAM86C2P
CABP2
NDUFV1
CDK2AP2
NUDT8
TBX10
CARNS1
PPP1CA
RAD9A
TMEM134
CORO1B
SSH3
ANKRD13D
ADRBK1
KDM2A
TBC1D10C
POLD4
CLCF1
GPR152
CABP4
RPS6KB2
C11orf72
RN7SKP239
PTPRCAP
DOC2GP
RN7SL59P
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16q22.2.

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

Genes
TXNL4B
HP
HPR
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q25.1.

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

Genes
ESR1
CCDC170
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q24.31.

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

Genes
SCARB1
DHX37
UBC
FAM101A
ZNF664
NCOR2
RPL22P19
MIR5188
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q26.13.

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

Genes
FGFR2
ATE1
WDR11
RN7SKP167
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5q35.2.

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

Genes
NSD1
ZNF346
FGFR4
Genes in Wide Peak

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

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

Genes
SMARCA4
DOCK6
LDLR
TSPAN16
C19orf80
YIPF2
C19orf52
CARM1
SPC24
KANK2
C19orf38
RN7SL298P
RN7SL192P

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 - 63 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
Xq24 2.6124e-19 1.046e-16 chrX:120007875-120081516 4
9q21.32 4.0103e-19 2.3987e-16 chr9:84303035-85595688 6
Xp11.23 4.3124e-30 2.3987e-16 chrX:49227385-49294531 1
Xq27.3 1.8098e-18 1.9494e-15 chrX:146280503-146993435 11
Xp11.23 1.0684e-23 8.6523e-11 chrX:49242802-49364868 8
22q13.2 4.2659e-10 4.2659e-10 chr22:42483231-42558040 2
12p13.33 2.372e-10 2.7336e-09 chr12:1-1023288 10
1q32.2 1.1481e-08 1.1481e-08 chr1:207640352-207832091 1
16p11.2 4.8533e-09 7.4774e-08 chr16:28606999-29096088 19
2q31.2 9.0217e-08 1.447e-07 chr2:179364010-179710350 1
3p12.2 1.447e-07 1.447e-07 chr3:79174698-85008837 3
2q13 2.8616e-08 2.5279e-07 chr2:114004548-114466229 6
15q24.2 1.9969e-08 4.2924e-06 chr15:75503089-75594075 4
7q11.23 4.442e-08 6.304e-06 chr7:74565114-74991226 1
14q32.31 9.7693e-06 9.7693e-06 chr14:101421561-101467109 7
4q21.21 1.1011e-05 6.0991e-05 chr4:80310909-81130806 7
19p13.3 4.7337e-06 6.506e-05 chr19:1271542-1391108 3
1p36.12 1.7823e-06 0.0001003 chr1:21616453-21929574 2
15q15.1 4.062e-08 0.0002726 chr15:41828850-42067588 3
19p13.2 7.7268e-07 0.0002726 chr19:10027488-10129404 1
16p13.3 4.2924e-06 0.00041389 chr16:1274666-1360359 4
17q24.1 0.00063565 0.0010392 chr17:62825077-62971926 4
11q24.2 0.0011898 0.0011898 chr11:125350042-125472047 1
10q25.3 0.00062462 0.0024298 chr10:118025223-118196378 1
Xp11.22 2.2575e-09 0.0024298 chrX:51729101-52699700 13
17p11.2 0.0034929 0.0034929 chr17:16340206-16946160 10
19p12 9.7073e-05 0.0034929 chr19:19770856-29698452 46
16q22.2 0.00076291 0.0050498 chr16:72052025-72130380 3
18q22.1 0.0067124 0.0071807 chr18:65178104-67512952 2
7p22.1 0.0113 0.0113 chr7:6647261-6757308 2
10q11.22 0.0082304 0.0113 chr10:46057438-49521432 42
19q13.33 0.012468 0.011865 chr19:48319867-48511909 4
15q26.3 1.687e-05 0.014369 chr15:101877940-102531392 12
11p15.3 0.00094887 0.018268 chr11:7110302-12932279 62
13q12.11 0.0063423 0.020402 chr13:21715137-21760631 3
11p15.5 0.0017945 0.022768 chr11:1-197414 1
1p36.32 4.2924e-06 0.029753 chr1:1-3380008 77
12q21.32 0.030796 0.031692 chr12:88404854-88542090 3
3p26.3 0.011865 0.036539 chr3:1-3194321 8
7q22.1 0.0021203 0.036539 chr7:101924076-102055787 3
9p24.1 0.027911 0.036539 chr9:7887780-14720087 10
20q13.13 0.040367 0.04154 chr20:48558306-48807557 4
4p15.31 0.044377 0.044377 chr4:17824605-20738601 3
9p24.3 0.012468 0.047671 chr9:1-846067 7
1p13.2 0.022241 0.053353 chr1:115323037-115582651 2
16p13.3 0.012904 0.062477 chr16:3521389-4015773 7
3q25.1 0.059791 0.06739 chr3:150663467-151143433 6
17q21.32 0.058016 0.076932 chr17:46642076-48610174 53
5q23.1 0.11032 0.11032 chr5:58153335-179527858 830
4q13.2 3.1319e-06 0.12834 chr4:69107098-70455087 10
7q22.1 0.028627 0.12834 chr7:99972120-100037371 3
3q25.33 0.11032 0.13081 chr3:159943122-160150304 3
7q11.21 0.044022 0.13081 chr7:57202402-65305587 23
16q22.1 0.0073817 0.13081 chr16:69140223-87117830 170
8p23.2 0.1531 0.16408 chr8:1-33236672 256
13q31.3 0.15181 0.16408 chr13:79978508-93884951 25
6q22.31 0.16665 0.16995 chr6:57084268-148602239 414
12p11.23 0.037304 0.21002 chr12:27234401-27852380 5
11p11.12 0.020386 0.22371 chr11:36611987-61733080 262
15q11.2 0.0003891 0.22371 chr15:1-38228522 142
20p13 0.22371 0.22371 chr20:3218711-3640486 4
13q12.11 0.1109 0.25448 chr13:1-74805964 359
3p21.1 0.014369 0.85551 chr3:1-198022430 1377
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq24.

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

Genes
CT47A10
CT47A9
CT47A12
CT47A11
Genes in Wide Peak

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

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

Genes
SPATA31D3
SPATA31D4
SNORD95|ENSG00000200969.1
SPATA31D1
SPATA31D5P
RNA5SP287
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp11.23.

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

Genes
GAGE2B
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq27.3.

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

Genes
MIR508
MIR510
MIR506
MIR514A2
MIR514A3
MIR514A1
MIR513B
MIR513A1
MIR507
MIR513A2
MIR514B
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp11.23.

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

Genes
GAGE2A
GAGE12G
GAGE12E
GAGE12H
GAGE12D
GAGE12F
GAGE12B
GAGE12C
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.2.

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

Genes
CYP2D6
CYP2D7P1
Genes in Wide Peak

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

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

Genes
KDM5A
SLC6A13
WNK1
SLC6A12
IQSEC3
CCDC77
B4GALNT3
NINJ2
FAM138D
RNU4ATAC16P
Genes in Wide Peak

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

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

Genes
CR1
Genes in Wide Peak

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

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

Genes
ATXN2L
SPNS1
NFATC2IP
CD19
RABEP2
SH2B1
TUFM
EIF3C
ATP2A1
SULT1A1
NPIPB9
LAT
snoU13|ENSG00000238352.1
snoU13|ENSG00000238684.1
snoU13|ENSG00000238699.1
SNORA43|ENSG00000252461.1
NPIPB8
MIR4721
MIR4517
Genes in Wide Peak

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

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

Genes
TTN
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p12.2.

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

Genes
GBE1
LINC00971
MIR3923
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q13.

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

Genes
CBWD2
RABL2A
WASH2P
FOXD4L1
FAM138B
RPL23AP7
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q24.2.

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

Genes
GOLGA6D
GOLGA6C
RN7SL489P
RN7SL327P
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q11.23.

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

Genes
GATSL2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.31.

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

Genes
SNORD113|ENSG00000200150.1
SNORD113|ENSG00000201036.1
SNORD113|ENSG00000201500.1
SNORD113|ENSG00000201710.1
SNORD113|ENSG00000222095.1
SNORD113|ENSG00000222185.1
SNORD112|ENSG00000252009.1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q21.21.

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

Genes
PRDM8
ANTXR2
GK2
SNORA75|ENSG00000212620.1
OR7E94P
LINC00989
PCAT4
Genes in Wide Peak

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

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

Genes
EFNA2
MUM1
C19orf24
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.12.

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

Genes
NBPF3
ALPL
Genes in Wide Peak

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

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

Genes
TYRO3
MGA
MIR626
Genes in Wide Peak

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

Table S66.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
COL5A3
Genes in Wide Peak

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

Table S67.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
TPSD1
TPSAB1
PRSS29P
TPSB2
Genes in Wide Peak

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

Table S68.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
LRRC37A3
AMZ2P1
SLC16A6P1
RN7SL404P
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q24.2.

Table S69.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
EI24
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q25.3.

Table S70.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CCDC172
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp11.22.

Table S71.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
MAGED4
XAGE2B
XAGE1C
XAGE2
MAGED4B
SSX7
XAGE1E
XAGE1D
XAGE1A
XAGE1B
SNORA11D
SNORA11E
RNA5SP504
Genes in Wide Peak

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

Table S72.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
TBC1D27
KRT17P1
ZNF287
CCDC144A
FAM211A
USP32P1
ZNF624
KRT16P2
TNFRSF13B
RN7SL620P
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19p12.

Table S73.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ZNF506
ZNF14
ZNF85
ZNF430
ZNF66
ZNF208
ZNF714
ZNF91
ZNF738
ZNF101
ZNF708
ZNF730
ZNF93
ZNF626
ZNF724P
ZNF676
ZNF681
ZNF493
ZNF729
ZNF431
ZNF429
ZNF100
ZNF682
ZNF257
ZNF98
ZNF675
ZNF43
RNA5SP469
RPSAP58
ZNF254
ZNF726
ZNF99
ZNF90
ZNF492
ZNF826P
ZNF737
snoU13|ENSG00000238514.1
RN7SL860P
RNA5SP470
ZNF486
ZNF253
LINC00662
LINC00663
LINC00906
LINC00664
ZNF728
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q22.2.

Table S74.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
TXNL4B
HP
HPR
Genes in Wide Peak

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

Table S75.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CCDC102B
TMX3
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7p22.1.

Table S76.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ZNF12
ZNF853
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q11.22.

Table S77.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ASAH2C
RBP3
GDF10
GDF2
ANXA8L1
FAM21B
ZNF488
ANXA8
FAM35BP
FRMPD2
FAM21C
ZFAND4
PTPN20B
ANXA8L2
AGAP4
FAM25C
FAM25B
FAM25G
AGAP9
ANTXRL
BMS1P5
AGAP10
NPY4R
GPRIN2
SYT15
BMS1P1
PTPN20A
RNA5SP314
LINC00842
GLUD1P2
FAM25E
RNA5SP311
RNA5SP310
ANTXRLP1
C10orf43
BMS1P2
RNA5SP315
RNA5SP313
RNA5SP312
RN7SL453P
RN7SL248P
RN7SL527P
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.33.

Table S78.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CRX
SULT2A1
BSPH1
TPRX2P
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q26.3.

Table S79.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
OR4F4
OR4F15
OR4F6
TM2D3
TARSL2
WASH3P
OR4F13P
snoU13|ENSG00000238502.1
RN7SL209P
DDX11L9
FAM138E
DNM1P47
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.3.

Table S80.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
LMO1
DKK3
MRVI1
RNF141
EIF4G2
GALNT18
STK33
SWAP70
LYVE1
AMPD3
MICALCL
SBF2
MICAL2
ADM
PPFIBP2
CYB5R2
TUB
RIC3
TRIM66
RPL27A
ST5
AKIP1
TMEM41B
ZNF143
WEE1
USP47
OR10A3
SYT9
TMEM9B
NRIP3
SCUBE2
EIF3F
OR10A6
ASCL3
C11orf16
OR10AB1P
NLRP10
OR5P3
OR5P2
OVCH2
OLFML1
DENND5A
PARVA
CTR9
SNORA3|ENSG00000200983.1
RN7SKP50
SNORA23
IPO7
SNORA45
RNU6ATAC33P
MIR302E
ZBED5
snoU13|ENSG00000238387.1
SNORD97
RN7SL56P
SCARNA16|ENSG00000252329.1
SCARNA20|ENSG00000252778.1
RNA5SP330
CSNK2A3
MTRNR2L8
MIR5691
MIR4299
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q12.11.

Table S81.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
SKA3
MRP63
RN7SL80P
Genes in Wide Peak

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

Table S82.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
SCGB1C1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.32.

Table S83.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PRDM16
TNFRSF14
CDK11A
NADK
PRKCZ
GNB1
SDF4
DVL1
MORN1
CPSF3L
ACAP3
C1orf159
MMEL1
C1orf222
PLCH2
FAM213B
PANK4
PEX10
RER1
SKI
ATAD3B
SSU72
UBE2J2
TTLL10
SCNN1D
MXRA8
C1orf86
ACTRT2
CALML6
TAS1R3
PUSL1
AURKAIP1
B3GALT6
LINC00982
FAM87B
TMEM52
VWA1
FAM132A
OR4F16
OR4F5
TNFRSF4
TNFRSF18
PLEKHN1
ISG15
SAMD11
C1orf170
GABRD
KLHL17
AGRN
HES4
NOC2L
SLC35E2B
MMP23B
MIB2
ATAD3A
HES5
MIR429
TMEM240
TMEM88B
MIR200A
MIR200B
SLC35E2
TTC34
ATAD3C
CCNL2
DDX11L1
GLTPD1
LINC00115
C1orf233
FAM41C
ANKRD65
OR4F29
RNF223
FAM138A
MRPL20
CDK11B
RN7SL657P
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q21.32.

Table S84.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
C12orf29
CEP290
RNA5SP364
Genes in Wide Peak

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

Table S85.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
TRNT1
IL5RA
CNTN6
CHL1
CNTN4
RN7SKP144
RN7SL120P
SNORA43|ENSG00000253049.1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q22.1.

Table S86.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
SH2B2
MIR548O
MIR4285
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p24.1.

Table S87.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
NFIB
TYRP1
MPDZ
PTPRD
LURAP1L
ZDHHC21
LINC00583
RN7SL849P
SNORD27|ENSG00000251699.1
RN7SL5P
Genes in Wide Peak

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

Table S88.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
SNAI1
LINC00651
TMEM189
UBE2V1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p15.31.

Table S89.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
SLIT2
LCORL
RNA5SP157
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p24.3.

Table S90.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
DOCK8
KANK1
FOXD4
CBWD1
C9orf66
FAM138C
RN7SL412P
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p13.2.

Table S91.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
TSHB
SYCP1
Genes in Wide Peak

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

Table S92.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CREBBP
CLUAP1
TRAP1
NLRC3
SLX4
DNASE1
C16orf90
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q25.1.

Table S93.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
GPR87
P2RY12
P2RY14
GPR171
P2RY13
RNA5SP145
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q21.32.

Table S94.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
COL1A1
PDK2
ITGA3
XYLT2
DLX3
NGFR
HOXB6
ABI3
DLX4
PPP1R9B
SGCA
MRPL27
LRRC59
HOXB8
HOXB5
SPOP
SLC35B1
FAM117A
CALCOCO2
RSAD1
MYCBPAP
CHAD
KAT7
EME1
PRAC
HOXB13
ATP5G1
UBE2Z
SNF8
IGF2BP1
GIP
B4GALNT2
GNGT2
PHB
SAMD14
TMEM92
ACSF2
HOXB9
TTLL6
PHOSPHO1
TAC4
NXPH3
HOXB4
HILS1
ZNF652
MIR196A1
SNORA68|ENSG00000212565.1
snoU13|ENSG00000238804.1
snoU13|ENSG00000239135.1
RN7SL125P
MIR10A
HOXB7
MIR3185
Genes in Wide Peak

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

Table S95.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
CD74
ITK
PDGFRB
APC
PIK3R1
EBF1
TLX3
NSD1
NPM1
RANBP17
CDKL3
SLC6A7
RNF14
MATR3
GABRA1
B4GALT7
FAM13B
DEPDC1B
RPL26L1
MFAP3
MAT2B
VCAN
ZFYVE16
SOX30
SPDL1
PHF15
LCP2
CTNNA1
YTHDC2
TSPAN17
NOP16
ERCC8
ADAMTS6
HEXB
PTCD2
COL23A1
THOC3
FSTL4
FAM114A2
CYFIP2
RIOK2
PRDM6
WNT8A
SLC12A2
SNX24
SNCAIP
ISOC1
KIF2A
PITX1
TRPC7
MAST4
NDST1
CAMK2A
TCOF1
AFF4
HMMR
P4HA2
STK10
FBXW11
CDHR2
SNCB
PKD2L2
KCNN2
TCF7
MEF2C
KIAA0141
PCDHB4
PCDHA6
PCDHGA2
MRPL22
GEMIN5
TNPO1
TAF9
SCAMP1
DIMT1
IPO11
FAT2
RBM22
ADAMTS2
UIMC1
RBM27
POU4F3
SEMA6A
GABRP
CDC23
ERBB2IP
PCDHB2
HARS2
NUDT12
MAN2A1
NME5
BRD8
KIF20A
HSPA9
MRPS27
PFDN1
HBEGF
SLC4A9
LOX
APBB3
TMCO6
SPARC
IK
HMGCR
COL4A3BP
FAF2
HAND1
PCDHB3
PCDHB5
PCDHB6
PCDHB7
PDE8B
CLK4
PCDHB15
HAVCR1
GRM6
RNF130
THG1L
ARSB
CLINT1
THBS4
IL12B
TTC1
MSH3
RASGRF2
GABRG2
CCNG1
POLR3G
LMNB1
ARRDC3
FAM172A
SLC27A6
LNPEP
PDE4D
IL4
RAD50
IL5
ST8SIA4
GNPDA1
PCDH12
SKP1
PPP2CA
FGF1
NR3C1
C5orf15
PPWD1
TRIM23
TRAPPC13
SEC24A
TXNDC15
RARS
WWC1
H2AFY
TCERG1
DPYSL3
SMAD5
CSNK1A1
HMGXB3
ERGIC1
CDX1
ATP6V0E1
BNIP1
STC2
CPEB4
HRH2
DBN1
ZNF346
UNC5A
ATP10B
ELL2
UBE2B
DUSP1
PANK3
MSX2
CYSTM1
WDR55
ARAP3
PCDHB8
PCDHB10
PCDHB14
PCDHB12
SLC25A2
ETF1
TGFBI
FAM53C
SIL1
PAIP2
MYOT
KDM3B
EGR1
POLK
SV2C
KIAA1191
NLN
CENPK
SLC36A1
IRF1
CANX
COX7C
IL17B
EPB41L4A
CDO1
REEP5
ZSWIM6
SLC34A1
F12
PRR7
PDLIM4
KIF3A
NDUFA2
ANKHD1
DIAPH1
NDFIP1
UBE2D2
MAP1B
CKMT2
ZCCHC9
MCCC2
REEP2
PCBD2
DMGDH
BHMT2
AP3B1
ZBED3
NMUR2
DCTN4
PDE6A
ANKRD32
LARS
SPINK5
HSD17B4
MRPS36
CCNB1
CDK7
CD180
CCNH
DOCK2
TMED7
NREP
WDR36
ADAM19
HAVCR2
CCNJL
FBN2
FAM159B
HAPLN1
LHFPL2
SSBP2
BHMT
ANKRD31
IQGAP2
CRHBP
RASA1
LIX1
GIN1
PPIP5K2
PAM
BDP1
GTF2H2
SLC30A5
BTF3
FBXL17
SPATA9
TSLP
TNFAIP8
FEM1C
COMMD10
ATG12
MEGF10
ADAMTS19
YIPF5
ARHGAP26
CXCL14
LECT2
SLC25A48
DDX46
IL9
TIMD4
RNF145
C1QTNF2
GABRA6
GABRB2
FBXO38
SPINK7
PCYOX1L
GLRA1
TNIP1
G3BP1
ZNF300
N4BP3
NHP2
RMND5B
BOD1
CPLX2
TENM2
KCNMB1
PCDHB18
PSD2
LRRTM2
ZMAT2
GFRA3
KLHL3
HIGD2A
FAM193B
RNF44
DOK3
CSNK1G3
SRFBP1
FER
ATG10
POC5
SPOCK1
FAM151B
JMY
HOMER1
XRCC4
CAMK4
TRIM36
SAR1B
CATSPER3
PART1
MARVELD2
RAD17
SREK1IP1
CWC27
SRP19
CENPH
CAST
CETN3
FAM81B
SREK1
CHD1
GRAMD3
ZCCHC10
LARP1
CNOT8
GRIA1
PPARGC1B
SLC26A2
LSM11
MED7
FGF18
PCDH1
SH3RF2
PPP2R2B
FCHO2
TMEM171
AFAP1L1
CDC25C
NRG2
HMHB1
CDC42SE2
RAPGEF6
FGFR4
HK3
C5orf45
SQSTM1
MGAT4B
MAML1
EDIL3
TMEM161B
ELOVL7
NDUFAF2
ZNF474
RNF180
GPR98
SLC25A46
STARD4
PGGT1B
F2RL2
CCDC112
C5orf63
PRRC1
F2RL1
AGGF1
WDR41
SCGB3A2
SPINK1
HTR4
GRPEL2
ARSK
RHOBTB3
TIGD6
SPZ1
SERINC5
ERAP1
ERAP2
CMYA5
TMEM174
CARTPT
PAPD4
ANKRA2
UBLCP1
FAM170A
UTP15
NSA2
GFM2
ACSL6
IL3
CSF2
SEPT8
SHROOM1
GDF9
UQCRQ
LEAP2
CREBRF
SFXN1
GALNT10
SAP30L
RPS14
MYOZ3
SLU7
PTTG1
CAMLG
FBXL21
RELL2
PHAX
ALDH7A1
UBTD2
FOXI1
ZNF608
PPIC
CEP120
PMCHL2
HNRNPH1
ZNF354A
IL13
RGS14
LMAN2
RAB24
PRELID1
SH3TC2
ADRB2
GPRIN1
STK32A
HINT1
DTWD2
FAM153A
SIMC1
NSG2
ADRA1B
FABP6
PWWP2A
FAXDC2
HARS
CD14
DNAJC18
SPATA24
MZB1
SLC23A1
NUDCD2
HSPA4
FAM71B
SGCD
MCC
TBCA
OTP
CXXC5
ENC1
S100Z
HDAC3
PCDHB1
SYNPO
SERF1A
SMN1
ACOT12
NIPAL4
FNDC9
DCP2
DMXL1
AQPEP
ABLIM3
GLRX
GPR151
PLAC8L1
MARCH3
SLCO4C1
FAM174A
RGMB
TMEM167A
SH3PXD2B
PHYKPL
PROP1
ARL10
CLTB
PCSK1
RFESD
MCTP1
NR2F1
EIF4E1B
LYSMD3
JAKMIP2
MBLAC2
SLC35A4
RUFY1
GCNT4
MTX3
ATOX1
HNRNPA0
AP3S1
ZNF354C
GPR150
SPINK6
ZNF366
ZNF454
ZNF354B
HTR1A
C5orf64
C5orf46
TAF7
F2R
C5orf30
FTMT
C5orf24
NEUROG1
KCNIP1
FAM153B
CSF1R
IGIP
ARHGEF37
DDX41
CCDC125
GTF2H2C
KCTD16
ARSI
SLIT3
EFNA5
TMEM173
PRR16
TMED9
DRD1
C5orf47
PURA
KIAA0825
C5orf50
LRRC70
PRELID2
SLC36A3
SLC36A2
KIAA1024L
RPS23
RGS7BP
LYRM7
TMEM232
PCDHB13
C5orf52
SPRY4
FBLL1
SMIM15
ANKDD1B
ANKRD34B
PFN3
GM2A
SPINK14
C5orf48
PDLIM7
PCDHB16
ANXA6
ZNF300P1
SLC22A4
TBC1D9B
SLC22A5
HNRNPAB
PCDHB11
C5orf56
OCLN
SGTB
FCHSD1
GRK6
CHSY3
CCDC69
TTC37
FAM169A
MIR4461
ZFP2
SOWAHA
PJA2
MIR340
MIR103A1
MIR378A
MIR3607
RNA5SP191
RNA5SP195
RNA5SP188
SNORD45|ENSG00000200051.1
RN7SKP145
RNA5SP197
SNORA27|ENSG00000200235.1
RNA5SP199
SNORA74A
RNA5SP192
RN7SKP246
RNA5SP194
RNA5SP189
RNY3P1
RNA5SP190
RN7SKP230
MIR582
CBY3
C5orf60
FAM153C
FAM196B
SPINK9
GRXCR2
PCDHGA1
PCDHA9
PCDHA8
PCDHA7
PCDHA5
PCDHA4
PCDHA2
PCDHA1
CCNI2
CTXN3
SNX2
SLCO6A1
NBPF22P
ATP6AP1L
SMN2
SERF1B
SNORA18|ENSG00000206592.1
SNORA70|ENSG00000206909.1
SNORA70|ENSG00000206958.1
SNORD63|ENSG00000206989.1
RNA5SP187
SNORA51|ENSG00000207177.1
RN7SKP62
MIR583
MIR585
MIR584
MIR143
GPX3
TSSK1B
U8|ENSG00000212249.2
SNORA40|ENSG00000212363.1
SNORA74B
SNORA57|ENSG00000212529.1
ZRSR1
LTC4S
MXD3
SRA1
VDAC1
NEURL1B
EFCAB9
SPINK13
ARHGEF28
MIR874
FNIP1
SNORA50|ENSG00000220986.1
U3|ENSG00000221043.1
MIR548P
MIR1229
MIR1294
MIR548F3
MIR1271
MIR1303
RNU6ATAC10P
RNU4ATAC2P
C5orf54
RN7SKP232
RN7SKP117
RN7SKP148
RNA5SP193
RNA5SP198
RN7SKP150
RN7SKP89
SNORD63|ENSG00000222937.1
RN7SKP68
FKSG52
HMGB3P22
GTF2H2B
NPY6R
KIF4B
PROB1
DHFR
ZNF879
C5orf58
C5orf27
CDKN2AIPNL
IRGM
snoU13|ENSG00000238334.1
SNORA13
snoU13|ENSG00000238369.1
snoU13|ENSG00000238400.1
snoU13|ENSG00000238451.1
snoU13|ENSG00000238605.1
snoU13|ENSG00000238688.1
snoU13|ENSG00000238740.1
snoU13|ENSG00000238745.1
snoU13|ENSG00000238796.1
SCARNA18|ENSG00000238835.1
SNORA47
snoU13|ENSG00000239011.1
snoU13|ENSG00000239026.1
snoU13|ENSG00000239067.1
snoU13|ENSG00000239084.1
snoU13|ENSG00000239103.1
snoU13|ENSG00000239159.1
snoU13|ENSG00000239191.1
PCDHA13
RN7SL87P
RN7SL782P
RN7SL255P
PCDHGC3
RN7SL541P
PCDHGC5
RN7SL629P
RN7SL791P
RN7SL655P
RN7SL68P
RN7SL646P
PCDHGC4
RN7SL169P
RN7SL868P
RN7SL177P
EIF4EBP3
PCDHAC2
RN7SL174P
TICAM2
RN7SL295P
RN7SL684P
RN7SL814P
RN7SL623P
RN7SL153P
LINC00461
LUCAT1
PCDHAC1
PCDHGB8P
POU5F2
PCDHA11
7SK|ENSG00000249352.3
NAIP
PCDHA14
MIR143HG
ECSCR
PCDHA10
AACSP1
LINC00491
LINC00492
C5orf20
FOXD1
PCDHA12
MIR2277
RN7SKP122
RNU4ATAC13P
SNORA31|ENSG00000251828.1
RN7SKP34
RN7SKP157
RNA5SP200
SNORA74|ENSG00000252213.1
snoU13|ENSG00000252295.1
SNORA31|ENSG00000252337.1
snoU13|ENSG00000252387.1
SNORA68|ENSG00000252458.1
RN7SKP70
RNU6ATAC36P
RNA5SP196
RN7SKP60
RNA5SP186
SNORA76|ENSG00000252904.1
RN7SKP64
RN7SKP57
SNORA40|ENSG00000253065.1
snoZ6|ENSG00000253067.1
RN7SKP295
PCDHGA12
GUSBP3
PCDHGB6
MIR4454
PCDHGA5
MIR146A
PCDHGA7
PCDHGA6
PCDHGA8
PCDHGA10
PCDHGA11
PCDHGB2
PCDHGB4
PCDHGB7
PCDHGB1
PCDHGA3
PCDHA3
PCDHB17
TIFAB
SMIM3
DND1
PCDHGA9
PCDHGB3
PCDHGA4
MIR378H
RN7SL689P
RN7SL439P
MIR4804
MIR3936
RN7SL711P
RN7SL476P
MIR378E
MIR4461
MIR3655
MIR4803
RN7SL71P
MIR3912
RN7SL802P
MIR3660
RN7SL208P
MIR5706
MIR4633
MIR3141
MIR5003
MIR3142
RN7SL867P
RN7SL9P
RN7SL378P
MIR4460
RN7SL339P
MIR4280
MIR5692C1
RN7SL103P
RN7SL562P
RN7SL682P
MIR4281
RN7SL616P
MIR5197
MIR3661
MIR4634
ARL14EPL
FLJ11235
CKS1B|ENSG00000268942.1
MIR145
MTRNR2L2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q13.2.

Table S96.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
YTHDC1
TMPRSS11E
UGT2B10
UGT2A3
UGT2B28
UGT2B4
UGT2B7
UGT2B15
UGT2B17
UGT2B11
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q22.1.

Table S97.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ZCWPW1
MEPCE
PPP1R35
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q25.33.

Table S98.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
IFT80
C3orf80
MIR15B
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q11.21.

Table S99.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ZNF92
ZNF117
INTS4L1
ZNF680
ZNF716
ZNF733P
ZNF107
ZNF138
ZNF679
ZNF273
SNORA63|ENSG00000200130.1
SNORA22|ENSG00000206634.1
SNORA15|ENSG00000206785.1
SNORA15|ENSG00000207062.1
SNORA22|ENSG00000207344.1
CCT6P1
INTS4L2
ZNF736
CCT6P3
SNORA63|ENSG00000252102.1
ZNF727
MIR3147
RN7SL855P
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q22.1.

Table S100.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
MAF
GABARAPL2
PHLPP2
BCAR1
ATP2C2
KARS
ADAT1
HSD17B2
PDPR
AARS
GLG1
NFAT5
DHODH
ZNF821
CYB5B
PSMD7
VAC14
COG4
FA2H
WDR59
MON1B
CMC2
MLYCD
NECAB2
HSDL1
TAF1C
WFDC1
COTL1
USP10
CRISPLD2
FOXF1
MTHFSD
PMFBP1
GAN
COX4I1
EMC8
GSE1
GINS2
NIP7
TERF2
VPS4A
MTSS1L
KLHL36
BCMO1
MPHOSPH6
CHST5
KIAA0513
DHX38
TXNL4B
MARVELD3
CHST4
ZFHX3
CLEC18B
ADAMTS18
NUDT7
GCSH
MBTPS1
CDH13
TLDC1
ADAD2
OSGIN1
IRF8
CIRH1A
NOB1
CNTNAP4
CFDP1
ZDHHC7
FAM92B
CMIP
DNAAF1
C16orf74
TMED6
CLEC18A
CLEC18C
DDX19B
ST3GAL2
FUK
IL34
HYDIN
ZNF19
CDYL2
CENPN
ATMIN
C16orf46
PKD1L2
CLEC3A
SLC38A8
AP1G1
LDHD
TMEM170A
TERF2IP
ZNF23
LINC00917
MLKL
RFWD3
KCNG4
DYNLRB2
CHTF8
SNTB2
DDX19A
CTRB1
CTRB2
VAT1L
CALB2
FOXL1
FOXC2
LINC00311
FTSJD1
NQO1
IST1
CHST6
ZFP1
SDR42E1
WWOX
ZNRF1
PKD1L3
SF3B3
NPIPB15
PDXDC2P
C16orf47
PLCG2
WWP2
TAT
RNA5SP430
RNA5SP432
RNA5SP433
SYCE1L
TMEM231
MIR140
COG8
SNORD111|ENSG00000221066.1
SNORD111B
RNU6ATAC25P
MIR1910
RNA5SP431
MIR1538
SNORD71
EXOSC6
ATXN1L
HSBP1
snoU13|ENSG00000238321.1
snoU13|ENSG00000238683.1
snoU13|ENSG00000238734.1
RN7SL520P
SNORD112|ENSG00000251700.1
RN7SKP190
SNORD33|ENSG00000252022.1
SNORA76|ENSG00000252122.1
SNORA62|ENSG00000252443.1
RN7SKP233
HP
PDF
7SK|ENSG00000260682.2
HCCAT5
MIR4720
HPR
CHTF8
RN7SL134P
SNORA70D
MIR3182
RN7SL381P
RN7SL407P
RN7SL279P
MIR5093
MIR4719
FENDRR
FLJ00418
PIH1
PKD1L2
FKSG63
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.2.

Table S101.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
PCM1
WRN
MTMR7
SLC7A2
RHOBTB2
EXTL3
STMN4
MYOM2
SLC18A1
MSR1
ADAM28
LZTS1
ADAM7
FGF20
FDFT1
ANGPT2
DPYSL2
PDGFRL
ZDHHC2
TRIM35
FZD3
INTS9
SH2D4A
INTS10
ERI1
SLC39A14
MTMR9
LEPROTL1
DCTN6
R3HCC1
GSR
TNFRSF10A
UBXN8
PPP2CB
ERICH1
NEFM
TUSC3
NEFL
ARHGEF10
KCTD9
FGL1
ASAH1
BNIP3L
DUSP4
CLU
TNFRSF10B
SORBS3
PTK2B
CHRNA2
ADRA1A
PPP3CC
PDLIM2
EPHX2
TUBBP1
MTUS1
XPO7
TEX15
TMEM66
LOXL2
ELP3
PEBP4
ADAMDEC1
BLK
GATA4
FAM86B2
MCPH1
MFHAS1
FBXO25
CSGALNACT1
ATP6V1B2
CCDC25
HMBOX1
GNRH1
BIN3
DOK2
SLC25A37
CHMP7
DOCK5
TDH
FAM167A
NEIL2
LONRF1
AGPAT5
MICU3
VPS37A
NAT2
PSD3
RBPMS
NRG1
NPM2
FGF17
DMTN
FAM160B2
KIAA1967
STC1
CTSB
DLC1
C8orf48
DEFA5
DEFA4
DEFA6
DEFB1
SPAG11B
SCARA3
PBK
SCARA5
PNOC
HR
REEP4
LGI3
SFTPC
BMP1
PHYHIP
POLR3D
GFRA2
LINC00208
XKR6
SOX7
C8orf74
ESCO2
NAT1
DEFB4A
PURG
ZNF596
TNKS
PPP1R3B
FAM86B3P
TNFRSF10D
TNFRSF10C
NUDT18
LPL
MSRA
OR4F21
KBTBD11
DEFB104A
DEFB103A
DEFB104B
DEFB103B
DEFB4B
MBOAT4
SLC35G5
SPAG11A
EGR3
TDRP
SGK223
CLN8
CSMD1
RP1L1
C8orf12
PRSS55
CDCA2
SGCZ
FAM86B1
XKR5
DEFB105A
DEFB107A
DEFB106A
DEFB105B
ZNF395
DEFB106B
NUGGC
PIWIL2
ENTPD4
GTF2E2
KIF13B
DLGAP2
DEFB107B
CNOT7
MIR383
RNA5SP258
RNA5SP263
RNA5SP260
SNORA62|ENSG00000201157.1
RNA5SP259
DEFB134
DEFB135
DEFB136
DEFA1
SNORA70|ENSG00000206661.1
SNORA67|ENSG00000207027.1
SNORA70|ENSG00000207244.1
MIR598
MIR597
MIR596
MIR320A
RNA5SP256
RNA5SP252
FBXO16
FP15737
ZNF705D
FAM90A24P
ZNF705B
ZNF705G
FAM66B
MIR548I3
MIR548H4
EBF2
PPP2R2A
RNA5SP261
RNA5SP251
RN7SKP159
USP17L2
RPL23AP53
FAM66E
FAM66A
SDAD1P1
DEFB130|ENSG00000232948.1
DEFB130|ENSG00000233050.1
LINC00529
snoU13|ENSG00000238466.1
snoU13|ENSG00000238496.1
snoU13|ENSG00000238624.1
snoU13|ENSG00000239065.1
DEFA3
RN7SL303P
DEFA1B
PNMA2
RN7SL651P
C8orf58
RN7SL318P
RN7SL293P
KIAA1456
LINC00589
U3|ENSG00000251944.1
RNA5SP253
RNA5SP255
RNA5SP262
RNA5SP254
U3|ENSG00000252543.1
SNORD112|ENSG00000252565.1
LINC00599
FAM183CP
SMIM18
PRSS51
FAM85B
CLDN23
ALG1L13P
PINX1
FAM66D
C8orf49
LINC00681
SOX7
MIR4660
RN7SL178P
MIR4286
RN7SL474P
RN7SL781P
MIR5692A2
RN7SL872P
MIR3148
MIR3622B
MIR4288
MIR548V
MIR4287
MIR4659A
LRLE1
Genes in Wide Peak

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

Table S102.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
NDFIP2
SPRY2
SLITRK5
SLITRK1
GPC5
SLITRK6
SNORD38|ENSG00000200733.1
MIR622
PTMAP5
MIR17HG
LINC00351
MIR4500HG
LINC00433
LINC00379
LINC00410
LINC00333
LINC00440
LINC00353
RNU4ATAC3P
RNA5SP34
LINC00564
LINC00559
LINC00560
MIR548AS
MIR4500
Genes in Wide Peak

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

Table S103.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
GOPC
ROS1
PRDM1
TNFAIP3
MYB
FUCA2
SLC22A16
IBTK
REV3L
VTA1
FYN
HIVEP2
PGM3
RWDD2A
UFL1
IL20RA
CCDC28A
RRAGD
HSF2
SEC63
IFNGR1
TBPL1
BCLAF1
PEX3
HEBP2
METTL24
TRAF3IP2
ATG5
SNAP91
CYB5R4
ME1
TRMT11
TUBE1
EPB41L2
RIMS1
MOXD1
STX7
DDX43
SESN1
OSTM1
FAM135A
COL19A1
DOPEY1
LYRM2
BCKDHB
PREP
HACE1
VNN3
ECHDC1
COL12A1
FRK
DSE
RWDD1
RSPH4A
SMIM8
CEP85L
ASF1A
MCM9
FAM184A
RNGTT
MAN1A1
GABRR2
SERINC1
HDDC2
TPD52L1
HINT3
NCOA7
MDN1
BACH2
FHL5
GPR63
KHDRBS2
FBXL4
CCNC
PRDM13
PTP4A1
SIM1
ASCC3
BVES
COL9A1
MED23
WASF1
AIM1
VNN1
VNN2
SMAP1
RPS12
B3GAT2
EYA4
SOBP
NR2E1
SNX3
HBS1L
PEX7
ZBTB24
FIG4
PERP
KIAA1244
SLC16A10
HECA
GPR126
PHACTR2
EPM2A
COX7A2
TMEM30A
SENP6
IMPG1
TTK
WISP3
LAMA4
FAM46A
TBX18
ELOVL4
FILIP1
CASP8AP2
HMGN3
UBE3D
CNR1
SPACA1
PHF3
ZC2HC1B
ADGB
PLAGL1
FBXO30
AKAP7
RAB32
ALDH8A1
SGK1
RNF146
ARG1
CTGF
TCF21
FOXO3
ARMC2
SLC17A5
OGFRL1
COL10A1
AMD1
NDUFAF4
USP45
RTN4IP1
QRSL1
C6orf203
COQ3
PNISR
POPDC3
MTO1
BAI3
ANKRD6
HTR1B
KHDC1
KIAA1009
SYNCRIP
SNX14
NT5E
MRAP2
EPHA7
AKIRIN2
ORC3
LCA5
MAP3K7
CGA
GJA10
LTV1
MAP7
CD164
LACE1
NHSL1
AHI1
HEY2
PKIB
TAAR5
NMBR
SMPD2
MICAL1
REPS1
STX11
PRIM2
LGSN
TPBG
IRAK1BP1
PHIP
PRSS35
MMS22L
FAXC
GABRR1
PNRC1
PM20D2
RARS2
SCML4
TBC1D32
CLVS2
GPR6
RNF217
RSPO3
ARHGAP18
TAAR2
TAAR6
TAAR8
ABRACL
TAAR1
SLC18B1
MTFR2
SLC2A12
SHPRH
AIG1
MCHR2
GJA1
UTRN
GRM1
PTPRK
ZUFSP
NUS1
C6orf57
ENPP3
SRSF12
AK9
CDK19
GTF3C6
MARCKS
EEF1A1
CD109
GJB7
SLC35A1
GRIK2
MB21D1
FABP7
TXLNB
CITED2
FAM26D
DCBLD1
SAMD3
TMEM200A
IL22RA2
PDSS2
STXBP5
LMBRD1
CDC40
HTR1E
SF3B5
VGLL2
PDE7B
FUT9
MANEA
SMPDL3A
THEMIS
KIAA1919
GPRC6A
TRAPPC3L
OLIG3
FAM26E
BEND3
NT5DC1
TAAR3
OR2A4
SLC35D3
CEP57L1
FAM162B
POU3F2
C6orf58
RFX6
PPIL6
KCNQ5
KLHL32
TRDN
TSPYL4
LIN28B
EYS
NKAIN2
FAM26F
ZNF292
ADAT2
TSPYL1
KIAA0408
SLC35F1
LAMA2
MYO6
HDAC2
KPNA5
MAP3K5
RPF2
ENPP1
FKBP1C
SH3BGRL2
PLN
UBE2J1
L3MBTL3
MIR30C2
RNA5SP218
RN7SKP163
RN7SKP211
RNA5SP214
RNA5SP215
U3|ENSG00000200492.1
SNORA33|ENSG00000200534.1
RN7SKP245
SNORA27|ENSG00000201807.1
SNORA33|ENSG00000202283.1
RNA5SP211
SAMD5
GJE1
ECT2L
TMEM244
CENPW
FAM229B
DDO
CCDC162P
LINC00222
LINC00577
C6orf164
C6orf163
SNHG5
RIPPLY2
OOEP
KHDC3L
DPPA5
SNORD101
SNORA70|ENSG00000206886.1
MIR587
MIR588
MIR548A2
MIR30A
MIR548B
MIR548U
SNORD65|ENSG00000212229.1
RNA5SP219
RNA5SP213
RNA5SP210
RNA5SP212
SNORA40|ENSG00000212587.1
COX5BP2
C6orf165
SOGA3
LINC00680
PRELID1P1
ZNF259P1
U3|ENSG00000221332.1
U3|ENSG00000221345.1
U3|ENSG00000221455.1
SNORD100
RN7SKP110
SNORA73|ENSG00000222145.1
RN7SKP56
RN7SKP51
RN7SKP106
RNA5SP222
RNA5SP209
RNA5SP221
TSTD3
LINC00326
LINC00271
LINC00472
SIGLECP3
CTAGE9
TAAR9
MIR2113
snoU13|ENSG00000238464.1
snoU13|ENSG00000238474.1
snoU13|ENSG00000238563.1
snoU13|ENSG00000238628.1
snoU13|ENSG00000238631.1
snoU13|ENSG00000238747.1
snoU13|ENSG00000238775.1
snoU13|ENSG00000238938.1
snoU13|ENSG00000238974.1
snoU13|ENSG00000238999.1
snoU13|ENSG00000239015.1
snoU13|ENSG00000239095.1
snoU13|ENSG00000239132.1
RN7SL11P
RN7SL564P
RN7SL415P
RN7SL183P
RN7SL617P
RN7SL797P
RN7SL643P
C6orf183
RN7SL47P
HS3ST5
RFPL4B
RNA5SP217
RN7SKP18
RNA5SP216
RNA5SP208
RNA5SP220
SNORA18|ENSG00000252249.1
SNORD112|ENSG00000252476.1
RN7SKP209
SNORD112|ENSG00000252932.1
SNORA73|ENSG00000253090.1
U3|ENSG00000253091.1
PBOV1
SOGA3
C6orf3
MTRNR2L9
SMLR1
KHDC1L
RN7SL509P
MIR3668
MIR4463
MIR4643
RN7SL336P
MIR4465
MIR548AI
MIR548AJ1
MIR3144
MIR4282
MIR3145
MIR4464
MIR548H5
RN7SL408P
7SK|ENSG00000271765.1
U6|ENSG00000272445.1
C6ORF165
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p11.23.

Table S104.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ARNTL2
PPFIBP1
SMCO2
REP15
STK38L
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p11.12.

Table S105.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
DDB2
EXT2
CREB3L1
TMEM132A
SYT7
CD6
PRDM11
SYT13
NR1H3
NUP160
TTC17
ALX4
SPI1
MS4A12
CD82
FOLH1
MTCH2
FNBP4
P2RX3
LPXN
DTX4
OSBP
MS4A6A
MS4A4A
CCDC86
PRPF19
TMEM109
SLC15A3
CD5
ACCS
MDK
AMBRA1
MADD
PTPMT1
MAPK8IP1
CRY2
PEX16
KBTBD4
TRIM51
MYRF
LRP4
MYBPC3
ACP2
DAGLA
SLC43A3
TIMM10
GIF
APLNR
FADS2
TMEM258
TCN1
PHF21A
LRRC4C
HSD17B12
DGKZ
TNKS1BP1
GLYAT
SERPING1
OR5F1
SSRP1
SLC43A1
PTPRJ
C11orf49
ARFGAP2
CELF1
DAK
TMEM138
FADS1
ZP1
PLAC1L
MS4A3
CPSF7
MS4A2
TRIM48
OR8K1
OR5M9
PRG3
UBE2L6
ZDHHC5
MED19
GLYATL2
MS4A1
TSPAN18
CYB561A3
PPP1R32
GYLTL1B
PACSIN3
SLC39A13
PSMC3
RAPSN
AGBL2
TRIM51HP
API5
ALKBH3
C11orf74
YPEL4
FAM111A
GLYATL1
OR4D6
PATL1
STX3
MRPL16
MS4A6E
MS4A7
MS4A14
MS4A5
MS4A8
MS4A15
OR8J3
OR5I1
SDHAF2
DDB1
VPS37C
VWCE
RAB3IL1
BEST1
FEN1
OR8I2
OR4C11
OR8U1
OR4X2
C1QTNF4
OR10V1
OR5A1
OR5A2
OR5B12
OR5B2
OR9I1
OR6Q1
CLP1
OR9G4
OR5AR1
OR5AP2
OR8J1
OR5T3
MS4A10
OR4D9
OR5B3
OR10W1
OR1S1
OR9G1
OR5M3
OR5R1
OR5J2
OR10AG1
OR4S2
ZNF408
CKAP5
ARHGAP1
ATG13
CHST1
TP53I11
OR4B1
OR4D11
OR5AN1
OR4C5
OR4C3
OR4S1
OR4X1
F2
HARBI1
OR10Q1
CHRM4
OR5AK2
OR5M8
OR8K3
OR8H1
OR5T1
OR5T2
OR8K5
OR8H3
OR8H2
OR5AS1
SLC35C1
OR4C6
OR4P4
OR4C16
OR4C15
OR4A15
OR4A16
LINC00301
TRIM49B
PTGDR2
LRRC55
OR4C46
OR5D14
OR5L1
OR5D18
OR9Q1
OR9Q2
PRG2
ZFP91
RTN4RL2
TMEM216
C11orf96
OR5W2
FAM111B
FAM180B
MPEG1
OR5B17
OR1S2
OR5B21
CTNND1
OR5D13
LRRC10B
MS4A13
OR5G5P
OR5D16
OR5L2
ACCSL
MIR611
MIR130A
C11orf31
MIR670
SNORD67|ENSG00000212135.1
TMX2
NDUFS3
MS4A18
MS4A4E
OOSP1
SMTNL1
TRIM64C
OR4A5
OR4C12
FADS3
MIR1908
RN7SKP259
RN7SKP192
PGA4
PGA3
KBTBD4
BTBD18
C11orf94
OR4A47
snoU13|ENSG00000238692.1
RN7SL23P
CNTF
RPLP0P2
HNRNPKP3
SNORA31|ENSG00000251838.1
RNA5SP341
RN7SKP287
SNORD67|ENSG00000252427.1
snoU13|ENSG00000252447.1
RNA5SP340
OR4D10
GLYATL1P2
OR5M10
OR5M1
OR5M11
PGA5
OR4C13
MIR5582
MIR3161
RN7SL435P
RN7SL42P
MIR4688
MIR3162
MIR4487
RN7SL652P
MIR4488
RN7SL772P
Genes in Wide Peak

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

Table S106.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
AQR
APBA2
CYFIP1
OCA2
FAM189A1
TJP1
UBE3A
EMC4
HERC2
SNRPN
MEIS2
DPH6
KATNBL1
EMC7
TRPM1
NIPA2
HERC2P2
SLC12A6
TUBGCP5
GOLGA8I
GOLGA8F
GJD2
ACTC1
GABRB3
CHRFAM7A
MTMR10
SCG5
GREM1
AVEN
OTUD7A
KLF13
NIPA1
GOLGA6L2
GOLGA8A
CHRNA7
GOLGA8EP
LPCAT4
ULK4P3
GOLGA8Q
MKRN3
GOLGA8J
HERC2P3
NOP10
GABRG3
PGBD4
NDN
OR4M2
GOLGA8G
OR4N4
NUTM1
CHRM5
NDNL2
GOLGA8DP
NPAP1
C15orf41
GABRA5
GOLGA8R
WHAMMP3
ARHGAP11B
GOLGA8M
GOLGA6L1
ZNF770
FAN1
ARHGAP11A
RYR3
RNA5SP391
GOLGA8O
HERC2P9
ATP10A
SNORA18|ENSG00000206849.1
U8|ENSG00000206987.1
U8|ENSG00000207430.1
U8|ENSG00000207432.1
MIR211
SNORD77|ENSG00000212415.1
SNORD115|ENSG00000212428.1
U3|ENSG00000212511.1
SNORA48|ENSG00000212604.1
SNURF
GOLGA8B
TMCO5B
GOLGA6L6
MIR1268A
RNA5SP390
CSNK1A1P1
SNHG14
POTEB2
GOLGA8N
POTEB
snoU13|ENSG00000238342.1
U8|ENSG00000238519.1
snoU13|ENSG00000238615.1
snoU13|ENSG00000238960.1
SNORD108
snoU13|ENSG00000239083.1
SNORD109B
RN7SL584P
RN7SL796P
RN7SL673P
RN7SL196P
RN7SL545P
RN7SL719P
RN7SL469P
RN7SL82P
RN7SL238P
RN7SL185P
RN7SL759P
RN7SL286P
RN7SL536P
RN7SL106P
RN7SL400P
RN7SL539P
RN7SL628P
RN7SL829P
RN7SL495P
WHAMMP2
FMN1
GOLGA8K
SNORA18|ENSG00000252425.1
U8|ENSG00000252602.1
snoZ278
MAGEL2
NBEAP1
CT60
LINC00929
CHEK2P2
ANP32AP1
PWRN1
ULK4P2
PWRN2
GOLGA8T
ULK4P1
GOLGA6L7P
GOLGA8S
GOLGA8H
MIR4510
MIR3942
MIR4508
MIR4715
DKFZP547L112
SNORD109A
SNORD64|ENSG00000270704.2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20p13.

Table S107.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
ATRN
C20orf194
U3|ENSG00000201346.1
RN7SL839P
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q12.11.

Table S108.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
FLT3
LCP1
BRCA2
RB1
CDX2
LHFP
AKAP11
MIPEP
IFT88
FRY
ATP12A
CPB2
DIS3
PIBF1
TDRD3
NUFIP1
PDS5B
KIAA0226L
HTR2A
FNDC3A
MLNR
CDADC1
CAB39L
KLF5
FGF9
SGCG
PARP4
SUPT20H
MRPS31
SLC25A15
KPNA3
FLT1
RGCC
VWA8
DGKH
KATNAL1
INTS6
DHRS12
MEDAG
TSC22D1
OLFM4
KLF12
PCDH17
ENOX1
TNFSF11
MTRF1
SPG20OS
SOHLH2
DNAJC15
PROSER1
UFM1
WBP4
ELF1
SMAD9
HSPH1
KBTBD7
ALG5
EXOSC8
PSPC1
ZMYM2
GJB6
GJA3
RPL21
MTIF3
GTF3A
RASL11A
UBL3
LINC00544
CCDC70
SPRYD7
EBPL
ATP7B
ZC3H13
GUCY1B2
TNFRSF19
RNF6
ATP8A2
MTUS2
ZMYM5
USPL1
XPO4
TPTE2
POMP
CDK8
ALOX5AP
WASF3
RNF17
GPR12
DCLK1
CCNA1
COG6
SPG20
RXFP2
EPSTI1
TRPC4
POSTN
RFXAP
TPT1
KIAA1704
STOML3
KL
RFC3
STARD13
NEK3
PCDH8
VPS36
RNASEH2B
CKAP2
LECT1
THSD1
BORA
LRCH1
SUCLA2
RCBTB1
MED4
PHF11
COG3
ITM2B
NUDT15
RCBTB2
SETDB2
NUPL1
MTMR6
SLC46A3
SLC7A1
PDX1
LNX2
N4BP2L1
SMIM2
WDFY2
HNRNPA1L2
LPAR6
ESD
DIAPH3
KLHL1
N6AMT2
LATS2
SAP18
FAM124A
FREM2
FOXO1
CCDC122
SERP2
SACS
PABPC3
CENPJ
CYSLTR2
ARL11
USP12
PAN3
SUGT1
GJB2
CRYL1
SKA3
MICU2
AMER2
KBTBD6
DACH1
FAM194B
TPTE2P5
GSX1
IL17D
NAA16
NBEA
MRP63
LRRC63
SPERT
SLC25A30
TEX26
DLEU1
LACC1
FAM216B
CSNK1A1L
KCTD4
ATP5EP2
SERTM1
MAB21L1
SHISA2
ZDHHC20
SPATA13
URAD
PCDH9
DLEU7
POLR1D
B3GALTL
GTF2F2
NHLRC3
ZAR1L
HMGB1
MPHOSPH8
ANKRD20A19P
NEK5
PCDH20
TUBA3C
KCNRG
SNORA25|ENSG00000199196.1
RNA5SP26
SNORA9|ENSG00000199282.1
SNORA31|ENSG00000199477.1
RNY4P24
RNY3P2
RNA5SP32
RNY4P9
RNY4P14
RNA5SP27
RNA5SP28
RNY1P1
RN7SKP6
RNY4P28
RN7SKP1
RNA5SP30
MZT1
PRR20B
PRR20A
TRIM13
TPTE2P6
C1QTNF9B
RNY1P8
RNY3P5
RNY1P6
SNORA27|ENSG00000207051.1
RNY3P4
RNY1P4
RNY3P9
RNY1P7
RNY3P10
SNORD102
MIR621
MIR320D1
MIR759
SNORA16|ENSG00000212293.1
SNORD37|ENSG00000212377.1
SNORD116|ENSG00000212553.1
SIAH3
LINC00598
ARL2BPP3
RNY4P30
RNY4P29
RNA5SP25
RNA5SP29
RNA5SP31
RNY1P3
RN7SKP3
LINC00571
LINC00297
LINC00572
LINC00365
LINC00393
RPS4XP16
LINC00457
LINC00378
LINC00350
PHF2P2
LINC00424
LINC00371
LINC00348
LINC00423
PRR20D
LINC00434
LINC00355
LINC00352
LINC00392
LINC00448
LINC00459
LINC00366
LINC00362
LINC00358
PRR20C
EEF1DP3
LINC00388
LINC00400
LINC00364
ATXN8OS
LINC00332
LINC00395
LINC00349
LINC00441
DLEU2
LINC00387
LINC00415
LINC00442
LINC00327
MIPEPP3
LINC00462
LINC00284
HNRNPA1P30
PRR20E
LINC00444
LINC00458
LINC00330
ESRRAP2
LINC00345
LINC00445
LINC00545
LINC00427
LINC00421
LINC00398
LINC00426
snoU13|ENSG00000238408.1
snoU13|ENSG00000238455.1
snoU13|ENSG00000238483.1
snoU13|ENSG00000238651.1
snoU13|ENSG00000238665.1
snoU13|ENSG00000238878.1
snoU13|ENSG00000238893.1
snoU13|ENSG00000238932.1
SUGT1P3
C1QTNF9
RN7SL288P
RN7SL515P
RN7SL618P
RN7SL272P
RN7SL741P
CCDC169
RN7SL413P
RN7SL761P
RN7SL320P
RN7SL766P
RN7SL597P
RN7SL700P
N4BP2L2
SNORA68|ENSG00000251715.1
SNORD27|ENSG00000252128.1
RNA5SP24
MIR2276
RN7SKP2
RN7SKP5
RNY4P31
SNORA31|ENSG00000253051.1
SNORD36|ENSG00000253094.1
SERPINE3
ALG11
TPTE2P1
UTP14C
LINC00556
LINC00562
LINC00543
LINC00563
LINC00566
LINC00558
LINC00621
MIR4704
MIR548X2
RN7SL80P
MIR4499
MIR4305
MIR5006
MIR3168
MIR5007
MIR3613
RN7SL289P
RN7SL166P
RN7SL375P
RN7SL49P
MIR5693
MIR4703
MIR3169
LSP1|ENSG00000269099.1
7SK|ENSG00000271818.1
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p21.1.

Table S109.  Genes in bold are cancer genes as defined by The Sanger Institute: Cancer Gene Census[7].

Genes
TFRC
MLH1
BCL6
TFG
CBLB
FOXP1
PIK3CA
RAF1
PPARG
VHL
FANCD2
LPP
XPC
EIF4A2
GMPS
RPN1
BAP1
PBRM1
CTNNB1
MYD88
MLF1
GATA2
SOX2
SETD2
FOXL2
MITF
FHIT
SRGAP3
ETV5
SEMA3F
RBM5
PLXND1
RBM6
ZMYND10
CACNA2D2
DLEC1
CELSR3
SS18L2
SEC62
UQCRC1
HHATL
PHF7
SEMA3G
NISCH
STAB1
ABHD5
LARS2
SEMA3B
LTF
SLC7A14
CLDN11
ACPP
CHDH
GLT8D1
ATP2C1
WWTR1
ALAS1
ARHGAP31
SLC4A7
ASTE1
TBC1D23
CASR
LSG1
PARP3
DCUN1D1
EPHA3
CP
MAP4
POLQ
PIK3CB
MCF2L2
ITIH4
ITIH1
IL17RB
DCBLD2
USP13
ATP11B
SEC61A1
DGKG
ACAA1
TNK2
ST3GAL6
POU1F1
ROPN1
PDIA5
NDUFB4
MYLK
CLDN18
ZBTB11
RHOA
HYAL2
RASSF1
IP6K2
IFT80
ATP1B3
PFN2
ZXDC
RAD18
LMCD1
HLTF
TRNT1
SIDT1
MCM2
TP63
PPP2R3A
IGF2BP2
MAP3K13
ST6GAL1
MGLL
FNDC3B
PLD1
DLG1
RAB7A
EXOSC7
MKRN2
PTPN23
RARB
TOP2B
MCCC1
LAMP3
LXN
CRYBG3|ENSG00000080200.5
EPHA6
CPOX
CLDND1
IMPG2
PCNP
UBA5
SEMA5B
GSK3B
ITGB5
RNF13
CHMP2B
MYNN
MECOM
DOCK3
C3orf18
TMEM40
KIF9
PCBP4
SI
FETUB
DNAJB11
LEPREL1
THPO
CHRD
IL5RA
CMTM6
TF
CDV3
CD200
CCDC80
DAZL
LRRFIP2
SEC22C
XYLB
EHHADH
CNTN3
SMC4
SELK
ACTR8
TBCCD1
TIMMDC1
CRBN
KNG1
HRG
HGD
CLDN16
ARL6
NPHP3
CD86
AMOTL2
NIT2
FAM162A
OGG1
KPNA1
PCCB
ARMC8
CEP70
RBP2
RBP1
SLC25A36
GRK7
RNF7
TFDP2
XRN1
KAT2B
BCHE
SERPINI2
PDCD10
LRRC31
WNT5A
PFKFB4
COL7A1
FGF12
PRKAR2A
HES1
USP4
ACAP2
ECT2
GNAT1
GNAI2
HYAL1
TUSC2
NPRL2
RPL24
CYB561D2
C3orf14
FXR1
BBX
IFT57
GNB4
HHLA2
IQCG
GBE1
MORC1
UMPS
NCBP2
SNX4
C3orf52
FRMD4B
SLC41A3
ROPN1B
PLXNA1
ATP6V1A
ABTB1
PODXL2
UPK1B
CSPG5
KLHL18
SCAP
EFCC1
KIAA1257
NEK11
MRPL3
PLSCR4
HEMK1
CISH
MAPKAPK3
ACVR2B
WDR48
COMMD2
GORASP1
PEX5L
RRP9
ABCC5
AADAC
ABHD14B
EIF1B
ARHGEF26
KLHL24
PLCH1
VIPR1
DNAH1
SSR3
ZBTB47
TNNC1
NKTR
CLCN2
EIF4G1
SPCS1
NEK4
STAG1
A4GNT
RARRES1
MFSD1
PIGZ
SENP5
SERP1
PLS1
PDZRN3
SEC22A
CSTA
DPPA4
POPDC2
B4GALT4
NAA50
CD80
ACKR5
CCR2
GHSR
TNFSF10
ZNF639
SLITRK3
FYTTD1
EMC3
SSUH2
TMEM115
MASP1
ATP13A4
HRASLS
ACKR4
ANAPC13
MBD4
SGOL1
MRPS25
SH3BP5
HACL1
TBC1D5
CAPN7
RFTN1
C3orf20
ZFYVE20
GALNT15
SLC6A6
DHX30
SLC6A11
NUP210
EEFSEC
HMGB1P5
ATP13A3
IRAK2
CAMK1
THUMPD3
BHLHE40
ARL8B
EDEM1
CNTN6
CHL1
VILL
FLNB
RTP4
ACTL6A
NDUFB5
MRPL47
TRA2B
SKIL
DBR1
DNAJC13
GPR87
SLC35A5
DIRC2
SENP7
GUCA1C
CCDC54
COX17
PARP9
SUMF1
CPNE9
TAMM41
VGLL4
RAB5A
GRIP2
EAF1
CNTN4
DYNC1LI1
RBMS3
GADL1
OSBPL10
GTDC2
ACKR2
FAM198A
CSRNP1
SLC25A38
ITGA9
SLC22A14
GOLGA4
CTDSPL
STAC
IQSEC1
CAND2
RPL32
PTPRG
IL17RD
SHQ1
SLC25A26
UBA3
ARL6IP5
TMF1
LRIG1
LRTM1
LIMD1
ZNF660
NFKBIZ
COL8A1
NXPE3
GPR128
MYH15
PHLDB2
ABHD10
TAGLN3
PLA1A
RABL3
ADPRH
IGSF11
ATG3
NR1I2
BOC
SRPRB
TMEM108
AGTR1
MED12L
EIF2A
ALDH1L1
OSBPL11
TRPC1
NCEH1
SPATA16
TMEM44
KIAA0226
AMT
TCTA
NICN1
UCN2
VPRBP
MANF
CCDC39
STXBP5L
EAF2
ILDR1
TM4SF19
MUC4
EIF2B5
AHSG
ECE2
VWA5B2
ITPR1
THRB
NGLY1
OXSM
MAGI1
QTRTD1
DRD3
ZNF385D
SCHIP1
CCDC50
IGSF10
MBNL1
GPD1L
PLOD2
ZIC1
CPB1
FEZF2
CD96
CMTM7
FBXL2
UBP1
GTF2E1
GPR15
TOMM70A
ABI3BP
TNIK
TSEN2
WNT7A
CCDC174
FGD5
DPH3
OXNAD1
PLCL2
RAB6B
EPHB1
TRIM42
ACPL2
RASA2
VPS8
LHFPL4
BRPF1
RPUSD3
SST
TATDN2
GHRL
SEC13
EXOG
ATP2B2
LYZL4
SLC6A1
KLHL40
TIMP4
SYN2
CACNA1D
CACNA2D3
APPL1
NCK1
DZIP1L
MRAS
ESYT3
FAIM
CLSTN2
UROC1
CHCHD6
CCDC58
KALRN
ANO10
CCR5
NBEAL2
CCDC12
PTH1R
MYL3
DVL3
AP2M1
ABCF3
PCYT1A
BDH1
RPL29
ITIH3
DCP1A
CGGBP1
CLDN1
KBTBD8
FAM19A4
EOGT
LMOD3
POGLUT1
SLC15A2
EIF4E3
PROK2
C3orf30
LRRC58
FSTL1
NEK10
KIAA1524
EOMES
AZI2
TGFBR2
RETNLB
HDAC11
TRAT1
FBLN2
STT3B
CHCHD4
DPPA2
SERPINI1
CLASP2
PRKCI
EFHB
EIF5A2
SLC2A2
RPL22L1
PPM1L
RYBP
PPP4R2
CD200R1
GTPBP8
C3orf17
SPICE1
KIAA1407
CADPS
SYNPR
C3orf49
THOC7
ATXN7
PSMD6
PRICKLE2
ADAMTS9
FAM194A
CLRN1
TIPARP
CCNL1
PTX3
HESX1
DCLK3
SLMAP
RPP14
ABHD6
DNASE1L3
C3orf67
IL17RE
IL17RC
CRELD1
PRRT3
FANCD2OS
PCOLCE2
U2SURP
MTMR14
TTC14
PLSCR2
CPA3
GYG1
HPS3
TM4SF18
TOPBP1
RYK
SNRK
KIAA1143
KIF15
TGM4
ZDHHC3
CDCP1
CLEC3B
SLC6A20
LZTFL1
FYCO1
CCR1
RTP3
LRRC2
ELP6
FBXO40
DTX3L
ZNF148
NMNAT3
TPRA1
YEATS2
POLR2H
KLF15
CCDC37
CAMK2N2
LIPH
TMEM41A
SENP2
IFT122
RHO
C3orf65
RFC4
RPL39L
TKT
PRKCD
RFT1
SFMBT1
GNL3
FAM208A
ARHGEF3
ZDHHC19
SLC51A
UBXN7
RNF168
PIGX
MFI2
CDC25A
CAMP
ZNF589
FBXW12
PLXNB1
CCDC51
ATRIP
SHISA5
BSN
APEH
RNF123
CAMKV
MON1A
MST1R
RAD54L2
TEX264
GRM2
DUSP7
POC1A
PPM1M
WDR82
TRANK1
TTC21A
RPSA
ENTPD3
ULK4
SETD5
GLYCTK
NT5DC2
SMIM4
PDHB
PXK
KCTD6
ACOX2
FAM107A
MOBP
CX3CR1
XIRP1
SCN11A
ARF4
FILIP1L
SHOX2
IL12A
GFM1
SOX14
SLC35G2
ZBBX
HSPBAP1
NMD3
B3GALNT1
KCNAB1
P2RY12
SLC33A1
ARL13B
GP9
CNBP
NLGN1
BTD
ROBO1
P2RY1
TM4SF4
TM4SF1
TMEM42
ZNF35
MYRIP
ALCAM
ZPLD1
UBE2E1
PDCD6IP
GLB1
CRTAP
CMTM8
SETMAR
BFSP2
GPR27
MINA
LSM3
TMEM43
TRH
FAM86JP
MFN1
KCNMB3
JAGN1
TADA3
LRRC34
GAP43
LAMB2
USP19
QARS
LRRC15
NME6
SLC9C1
CXCR6
SUCLG2
KLHL6
ZMAT3
COL6A5
TMCC1
EFCAB12
RAB43
ZNF621
OXSR1
SLC22A13
FRG2C
GXYLT2
ARPP21
ADCY5
PARP14
PARP15
IQCB1
GOLGB1
TLR9
IQCF1
DAG1
CCDC36
SMARCC1
MST1
GMPPB
XCR1
CCR9
MUC13
SUSD5
HEG1
TOPAZ1
PHC3
GPR160
GOLIM4
XXYLT1
NRROS
CEP19
FBXO45
TRMT10C
ZNF80
GCSAM
IL20RB
MSL2
KY
SLCO2A1
NR1D2
RPL15
WDR49
DENND6A
PDE12
DNAH12
RSRC1
C3orf55
C3orf33
P2RY14
GPR171
GPR149
DHX36
ZIC4
CHST2
ATR
GK5
RTP1
SPSB4
ZNF654
MRPS22
CADM2
PSMD2
FAM131A
PARL
CCDC14
GPR156
RUVBL1
LRRN1
AMIGO3
TMPRSS7
IP6K1
TMEM39A
KIAA2018
B3GNT5
MUC20
ZBTB38
CCDC71
MAGEF1
NR2C2
ARIH2
ZBED2
TBL1XR1
ACAD9
NAALADL2
PVRL3
ZNF620
ZNF619
IMPDH2
ALS2CL
PRSS42
NDUFAF3
GRAMD1C
HTR3C
DALRD3
WDR6
P4HTM
SLC25A20
EPM2AIP1
NSUN3
DHFRL1
GP5
STX19
CPN2
H1FOO
ZNF852
C3orf38
HTR1F
TCAIM
DNAJB8
LSMEM2
ARL14
LRRC3B
RBM15B
CCR8
C3orf80
HCLS1
PAK2
CCDC66
CYP8B1
TPRXL
MB21D2
C3orf22
CHST13
MAP6D1
OXTR
GPR62
HIGD1A
ADIPOQ
NME9
TMEM45A
RAP2B
TMIE
P2RY13
ZBTB20
C3orf58
SIAH2
COPG1
SLC9A9
TIGIT
UBA7
UBE2E2
OTOL1
CEP97
CAV3
SATB1
EPHB3
TRAK1
RPL35A
CEP63
CNOT10
ZNF662
GABRR3
TMEM89
C3orf37
CCR3
PP13439
FAM19A1
TRAIP
CCR4
MAATS1
SCN5A
KCNH8
PP2D1
PPP1R2
CMSS1
ZDHHC23
IQCF2
ACTRT3
COPB2
PROS1
PRR23B
H1FX
ROBO2
FAM43A
ZNF445
SCN10A
SDHAP1
LSAMP
FAM212A
LMLN
WDR53
KLHDC8B
LRCH3
HTR3E
HTR3D
ARGFX
CIDECP
BTLA
TMEM212
KPNA4
ZNF501
ZNF197
SPATA12
HYAL3
SAMD7
C3orf70
PLCD1
CCK
CMC1
CIDEC
CDHR4
ATP13A5
ERC2
KBTBD12
TPRG1
PRSS45
TMPPE
LRRIQ4
PLSCR1
C3orf62
SLC38A3
PAQR9
OSTN
SNTN
RPL14
UTS2B
APOD
ALG1L
IL1RAP
OR5K4
GRM7
ZKSCAN7
CPNE4
TSC22D2
PIK3R4
SPTSSB
MME
OR5AC2
HRH1
ZNF502
CD47
WDR5B
ZNF860
VEPH1
ATG7
KCNMB2
TXNRD3
NKIRAS1
OR5H2
AADACL2
LEKR1
QRICH1
NUP210P1
TMEM207
RTP2
NUDT16
C3orf35
FAM3D
C3orf27
SUCNR1
OPA1
SELT
DZIP3
MIR425
MIR26A1
MIRLET7G
RN7SKP25
SNORA63|ENSG00000199363.1
RNA5SP124
SNORA43|ENSG00000199815.1
RNA5SP150
U3|ENSG00000199927.1
RNA5SP145
RNA5SP123
U3|ENSG00000200222.1
RNA5SP133
SNORA18|ENSG00000200288.1
SNORA63|ENSG00000200320.1
SNORA72|ENSG00000200355.1
RN7SKP45
SNORA63|ENSG00000200418.1
RNY4P4
RNA5SP139
SNORA63|ENSG00000201229.1
RNA5SP130
RN7SKP227
RNA5SP142
RNA5SP140
U8|ENSG00000201398.1
snoZ40
RNA5SP141
RNA5SP132
RN7SKP124
SNORA25|ENSG00000201701.1
RNA5SP125
U8|ENSG00000201810.1
RNA5SP149
SNORA33|ENSG00000201827.1
SNORA25|ENSG00000201957.1
RNA5SP126
RNA5SP138
RNA5SP128
U3|ENSG00000202268.1
RNA5SP131
SNORA62|ENSG00000202363.1
SNORA70|ENSG00000202379.1
RNA5SP151
SNORA64|ENSG00000202517.1
LINC00501
GMNC
DNAJC19
EGFEM1P
ANKUB1
PRR23A
C3orf72
COL6A6
TXNRD3NB
PTPLB
WDR52
CD200R1L
LNP1
OR5K3
VGLL3
PRSS50
TRIM71
ZCWPW2
ANKRD28
COLQ
METTL6
SNORA6
SNORA5
SNORA72|ENSG00000207084.1
SNORA7B
SNORD38|ENSG00000207109.1
SNORA24|ENSG00000207130.1
SNORA7A
MIR191
MIR570
MIR28
MIR551B
MIR568
MIR15B
MIR564
MIR563
MIR566
MIR135A1
MIR567
MIR569
RNU6ATAC4P
RNU6ATAC26P
SACM1L
MIR711
U8|ENSG00000212145.2
SNORD66|ENSG00000212158.1
U3|ENSG00000212211.1
SNORD69
SNORD19|ENSG00000212493.1
U3|ENSG00000212598.1
SNORA26|ENSG00000212608.1
TCTEX1D2
CRYGS
TRIM59
OR5AC1
TMEM110
NCKIPSD
TREX1
TTLL3
SMCO1
LINC00887
ALG3
IQCJ
FAM188B2
RPL39P5
C3orf56
LINC00488
IQCF5
IQCF6
IFRD2
MIR922
MIR944
MIR885
RNU6ATAC29P
RNU6ATAC6P
MIR1280
MIR1224
RNU6ATAC15P
MIR1263
MIR1284
SNORA81|ENSG00000221420.2
RNU6ATAC16P
MIR1226
U3|ENSG00000221633.1
MIR548I1
MIR720
MIR1324
ARIH2OS
SLC12A8
TMEM14E
C3orf36
RNA5SP129
SNORD19|ENSG00000222345.1
RNY5P3
RN7SKP177
RN7SKP61
RN7SKP222
RNA5SP146
RNA5SP144
RN7SKP212
RNA5SP136
RN7SKP284
RN7SKP58
RNA5SP127
RN7SKP144
RN7SKP296
LINC00691
LINC00620
LINC00885
C3orf83
SLC26A6
LINC00694
PRSS44
ANKRD18DP
LINC00606
ZNF717
LINC00693
LINC00578
COL6A4P2
KRT8P12
SPINK8
IQCF3
HSPD1P6
OR5H6
COL6A4P1
LINC00692
LINC00852
OR5H1
PLSCR5
OR5K2
TMA7
OR5K1
BPESC1
OR5H8P
LINC00884
GPX1
CRYBG3|ENSG00000233280.2
OR5H15
CYP2AB1P
LINC00690
PRR23C
TMEM30C
EGOT
OR5H14
FAM157A
C3orf84
LINC00312
C3orf79
snoU13|ENSG00000238312.1
snoU13|ENSG00000238345.1
snoU13|ENSG00000238350.1
snoU13|ENSG00000238359.1
SNORD61|ENSG00000238377.1
snoU13|ENSG00000238398.1
snoU13|ENSG00000238416.1
snoU13|ENSG00000238480.1
snoU13|ENSG00000238491.1
snoU13|ENSG00000238525.1
snoU13|ENSG00000238565.1
snoU13|ENSG00000238568.1
snoU13|ENSG00000238642.1
snoU13|ENSG00000238646.1
snoU13|ENSG00000238670.1
snoU13|ENSG00000238701.1
SCARNA7
SNORD19B|ENSG00000238862.1
snoU13|ENSG00000238874.1
snoU13|ENSG00000238891.1
snoU13|ENSG00000238902.1
snoU13|ENSG00000238905.1
snoU13|ENSG00000238929.1
SNORD2|ENSG00000238942.1
snoU13|ENSG00000238992.1
snoU13|ENSG00000239093.1
snoU13|ENSG00000239096.1
snoU13|ENSG00000239126.1
snoU13|ENSG00000239128.1
snoU13|ENSG00000239140.1
snoU13|ENSG00000239141.1
snoU13|ENSG00000239146.1
RN7SL271P
ASB14
RN7SL752P
LINC00879
TLR9
LINC00888
RN7SL567P
CPHL1P
GHRLOS
ACAD11
LINC00636
LINC00973
ISY1
KRBOX1
LINC00886
PLCXD2
RN7SL751P
RN7SL110P
LINC00881
RN7SL582P
LINC00877
TDGF1
RN7SL553P
CT64
LINC00903
RN7SL182P
LINC00635
RN7SL767P
ARPC4
RN7SL482P
RN7SL418P
RN7SL504P
RN7SL434P
RN7SL517P
LINC00969
RN7SL215P
TFP1
LINC00901
LINC00960
RN7SL294P
LINC00971
LINC00882
RN7SL229P
LINC00870
TUSC7
snoU13|ENSG00000243321.2
RN7SL738P
RN7SL815P
RN7SL141P
NAT6
RN7SL172P
LINC00880
MUSTN1
LINC00883
RN7SL647P
ACY1
RN7SL447P
FAM86DP
RN7SL397P
RN7SL120P
PBX2P1
RN7SL698P
RN7SL762P
RN7SL36P
LINC00698
RN7SL145P
RN7SL216P
CCDC13
RN7SL863P
MTHFD2P1
RN7SL724P
RN7SL870P
NUDT16P
TWF2
ABHD14A
SNORA58|ENSG00000249020.1
TMEM158
FGD5P1
ALG1L2
RPL32P3
SNORA4|ENSG00000251730.1
RN7SKP46
RN7SKP298
U3|ENSG00000251800.1
snoU13|ENSG00000251938.1
SNORD77|ENSG00000251967.1
SNORD63|ENSG00000251987.1
RN7SKP52
SNORD112|ENSG00000252170.1
RN7SKP265
RNA5SP134
RNA5SP147
RNA5SP148
SCARNA21|ENSG00000252409.1
snoU13|ENSG00000252435.1
RNY4P22
MIR2115
RNU6ATAC24P
RNA5SP137
RNA5SP143
SNORD19B|ENSG00000252787.1
RNA5SP135
RN7SKP234
SNORA31|ENSG00000252989.1
U8|ENSG00000253004.1
RN7SKP40
SNORA43|ENSG00000253049.1
SNORD112|ENSG00000253076.1
RNU4ATAC17P
SNORA81|ENSG00000253092.1
FAM86HP
PYDC2
BRK1
RPP14
EBLN2
LINC00696
PRSS46
RN7SL821P
MIR5193
MIR4788
MIR4270
RN7SL296P
MIR3919
RN7SL4P
SNORA4|ENSG00000263776.1
MIR4793
MIR4448
RN7SL147P
MIR3938
MIR5688
MIR4795
MIR4442
MIR5186
MIR3134
MIR5682
MIR378B
MIR4796
RN7SL859P
MIR4271
RN7SL217P
MIR3714
MIR3921
MIR4789
MIR5092
MIR4792
RN7SL486P
RN7SL321P
RN7SL664P
MIR4790
MIR3923
MIR4446
RN7SL411P
MIR548AB
MIR3137
MIR3136
MIR4447
MIR548AQ
MIR4443
RN7SL92P
RN7SL300P
MIR4797
MIR5704
MIR4445
MIR544B
ESRG
RN7SL703P
MIR5002
MIR4273
RN7SL637P
RN7SL773P
MIR3135A
LUZPP1
MTRNR2L12
NPCDR1
TERC
U7|ENSG00000271841.1
snoU13|ENSG00000271842.1
MIR4791
snoU13|ENSG00000271922.1
U1|ENSG00000272020.1
SNORD5|ENSG00000272166.1
U4|ENSG00000272359.1
MIR4787
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 41 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 Del z-score Del q-value
1p 1300 0.09 0.09 0.668 0.638 0.04 0.04 -1.15 0.998
1q 1195 0.27 0.28 7.42 2.58e-12 0.03 0.04 -1.16 0.998
2p 624 0.15 0.15 2.34 0.0376 0.01 0.01 -2.43 0.998
2q 967 0.14 0.14 2.26 0.0396 0.02 0.02 -1.95 0.998
3p 644 0.10 0.11 0.729 0.627 0.06 0.07 -0.635 0.998
3q 733 0.16 0.16 2.78 0.0117 0.01 0.01 -2.38 0.998
4p 289 0.01 0.01 -2.59 0.998 0.12 0.12 1.06 0.518
4q 670 0.00 0.00 -2.86 0.998 0.12 0.12 1.25 0.45
5p 183 0.05 0.05 -1.23 0.998 0.09 0.09 0.0864 0.998
5q 905 0.02 0.02 -2.04 0.998 0.11 0.11 1.11 0.518
6p 710 0.10 0.10 0.561 0.687 0.00 0.00 -2.88 0.998
6q 556 0.08 0.08 -0.208 0.994 0.01 0.01 -2.58 0.998
7p 389 0.13 0.14 1.63 0.158 0.05 0.06 -1.04 0.998
7q 783 0.14 0.15 2.26 0.0396 0.05 0.06 -0.845 0.998
8p 338 0.19 0.20 3.86 0.000274 0.07 0.09 -0.109 0.998
8q 551 0.20 0.21 4.23 6.22e-05 0.04 0.05 -1.17 0.998
9p 301 0.02 0.02 -2.17 0.998 0.14 0.14 1.81 0.225
9q 700 0.00 0.00 -2.79 0.998 0.16 0.16 2.71 0.0288
10p 253 0.25 0.26 5.83 4.09e-08 0.05 0.07 -0.736 0.998
10q 738 0.24 0.25 5.86 4.09e-08 0.04 0.05 -0.986 0.998
11p 509 0.03 0.03 -1.86 0.998 0.08 0.08 -0.171 0.998
11q 975 0.04 0.04 -1.33 0.998 0.07 0.07 -0.273 0.998
12p 339 0.10 0.10 0.49 0.707 0.04 0.04 -1.51 0.998
12q 904 0.10 0.10 0.809 0.599 0.04 0.04 -1.29 0.998
13q 560 0.06 0.07 -0.673 0.998 0.10 0.11 0.681 0.82
14q 938 0.07 0.07 -0.377 0.994 0.01 0.01 -2.48 0.998
15q 810 0.01 0.01 -2.42 0.998 0.13 0.13 1.75 0.225
16p 559 0.06 0.06 -0.786 0.998 0.06 0.06 -0.786 0.998
16q 455 0.05 0.05 -1.17 0.998 0.07 0.07 -0.498 0.998
17p 415 0.07 0.08 -0.272 0.994 0.13 0.14 1.73 0.225
17q 972 0.06 0.07 -0.541 0.998 0.08 0.09 0.162 0.998
18p 104 0.09 0.09 -0.0187 0.909 0.03 0.03 -1.98 0.998
18q 275 0.07 0.07 -0.581 0.998 0.05 0.05 -1.24 0.998
19p 681 0.07 0.07 -0.361 0.994 0.06 0.06 -0.703 0.998
19q 935 0.08 0.09 0.142 0.829 0.06 0.07 -0.558 0.998
20p 234 0.22 0.22 4.52 2.71e-05 0.01 0.01 -2.41 0.998
20q 448 0.22 0.22 4.7 1.41e-05 0.01 0.01 -2.35 0.998
21q 258 0.06 0.06 -0.946 0.998 0.05 0.05 -1.28 0.998
22q 564 0.08 0.09 0.145 0.829 0.12 0.13 1.5 0.321
Xp 418 0.08 0.10 0.318 0.768 0.19 0.21 3.97 0.00038
Xq 668 0.08 0.10 0.443 0.707 0.19 0.21 4.18 0.000211
Yp 70 0.14 0.26 4.25 6.22e-05 0.47 0.55 14.4 0
Yq 78 0.14 0.26 4.26 6.22e-05 0.47 0.55 14.4 0
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 = /cromwell_root/fc-8b2df640-93e1-40a2-b735-5b7a14ef6398/57cbe374-5642-4716-9266-1e4fd76b7e53/aggregate_data_workflow/46700a06-1391-46bd-ab9f-5a96ef57a919/call-aggregate_data/CPTAC3-UCEC-TP.CNV__wxs.seg.txt

  • Markers File = ./this_file_does_not_exist.txt

  • Reference Genome = /cromwell_root/broad-institute-gdac/gdc/reference/gistic/hg19_GENCODE_v18_20140127.mat

  • CNV Files = /cromwell_root/broad-institute-gdac/gdc/reference/gistic/SNP6.merged.151117.hg19.CNV.txt

  • Amplification Threshold = 0.1

  • Deletion Threshold = 0.1

  • Cap Values = 1.5

  • Broad Length Cutoff = 0.98

  • 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 100 Input Tumor Samples.

Tumor Sample Names
C3L-00006_TP
C3L-00008_TP
C3L-00032_TP
C3L-00090_TP
C3L-00098_TP
C3L-00136_TP
C3L-00137_TP
C3L-00139_TP
C3L-00143_TP
C3L-00145_TP

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.

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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