SNP6 Copy number analysis (GISTIC2) - Bladder Urothelial Carcinoma (Primary solid tumor)

SNP6 Copy number analysis (GISTIC2)

Bladder Urothelial Carcinoma (Primary solid tumor)

28 January 2016 | analyses__2016_01_28

Maintainer Information

Citation Information

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Cite as Broad Institute TCGA Genome Data Analysis Center (2016): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C16T0KXB

Overview

Introduction

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

Summary

There were 408 tumor samples used in this analysis: 30 significant arm-level results, 37 significant focal amplifications, and 36 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 - 37 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
6p22.3	7.0358e-82	7.0358e-82	chr6:21462625-21757620	2
1q23.3	6.2869e-56	6.1828e-49	chr1:161001146-161084006	7
11q13.3	2.1017e-45	1.777e-43	chr11:69464719-69481388	2
8q22.3	1.6131e-47	3.5745e-41	chr8:101746104-101995874	3
3p25.2	7.6031e-36	7.6031e-36	chr3:12384543-12494277	1
12q15	1.5107e-24	1.5107e-24	chr12:69178021-70150587	12
10p14	3.3503e-17	3.3503e-17	chr10:7924008-8345608	3
8p11.23	7.0205e-19	7.6629e-16	chr8:37449639-37645465	4
19q12	7.2449e-15	1.7046e-12	chr19:30290812-30528529	2
20q11.21	7.3224e-09	7.3224e-09	chr20:30109883-30332464	6
1p34.2	9.7487e-09	9.7487e-09	chr1:40039708-40539227	12
17q12	3.4505e-11	7.7764e-08	chr17:37830679-37899687	5
5p15.33	7.3103e-07	7.3103e-07	chr5:1-1962255	31
7p11.2	4.076e-09	9.8199e-07	chr7:54752424-55428978	3
1q21.3	3.5262e-28	3.8786e-05	chr1:150496857-150863520	13
13q22.1	0.00019023	0.00019023	chr13:73809522-74092438	1
7p21.1	1.6239e-06	0.00020836	chr7:16925519-17854266	3
16p13.2	6.162e-06	0.00034988	chr16:8524681-9597257	9
22q12.2	0.00055806	0.00055806	chr22:29404707-31755748	55
3q26.33	0.0018563	0.0018563	chr3:163842832-198022430	254
17q23.3	0.00012456	0.0024208	chr17:57049659-81195210	367
4p16.3	0.0031734	0.0031734	chr4:1738268-1817427	3
6q21	0.0051938	0.016021	chr6:107256674-107514789	3
4q13.3	0.021206	0.021206	chr4:73675242-74478903	9
2p25.1	0.033813	0.033813	chr2:1-10383874	50
11q22.2	4.0493e-06	0.046827	chr11:101984719-102817092	14
12p12.1	0.05329	0.05329	chr12:24880663-26135323	9
19q13.43	0.013691	0.060528	chr19:53202481-58657102	234
16q22.1	0.063591	0.063591	chr16:67091362-74472459	138
9p24.1	0.073854	0.073854	chr9:962233-9621486	46
6q23.3	0.057414	0.077908	chr6:135470481-135807204	3
11p13	0.084381	0.093343	chr11:33493973-35438140	16
8p11.21	7.4005e-05	0.13939	chr8:41509238-42133127	9
8q24.21	2.9785e-13	0.15486	chr8:127017284-129586945	13
16p11.2	0.040034	0.1633	chr16:28605319-29428538	24
17q11.2	1.6872e-05	0.2473	chr17:27064353-27933231	21
17p11.2	0.12737	0.2798	chr17:20571331-25270516	13

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p22.3.

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

Genes
LINC00340
SOX4

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q23.3.

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

Genes
F11R
PFDN2
USF1
PVRL4
KLHDC9
ARHGAP30
TSTD1

Genes in Wide Peak

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

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

Genes
CCND1
ORAOV1

Genes in Wide Peak

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

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

Genes
RN7SL685P
RNU6ATAC41P
YWHAZ

Genes in Wide Peak

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

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

Genes
PPARG

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q15.

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

Genes
MDM2
RN7SL804P
SLC35E3
CPM
LYZ
YEATS4
CCT2
FRS2
CPSF6
RAB3IP
BEST3
LRRC10

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10p14.

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

Genes
GATA3
LINC00708
TAF3

Genes in Wide Peak

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

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

Genes
ZNF703
ERLIN2
PROSC
GPR124

Genes in Wide Peak

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

Table S9. 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 20q11.21.

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

Genes
BCL2L1
ID1
TPX2
HM13
COX4I2
MIR3193

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p34.2.

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

Genes
BMP8B
MYCL
PPT1
PABPC4
PPIE
CAP1
HEYL
HPCAL4
TRIT1
OXCT2
NT5C1A
MFSD2A

Genes in Wide Peak

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

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

Genes
ERBB2
MIR4728
GRB7
MIEN1
PGAP3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p15.33.

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

Genes
NDUFS6
SDHAP3
MIR4635
ZDHHC11B
CCDC127
LRRC14B
PLEKHG4B
SDHA
SLC6A3
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
IRX4
CEP72
AHRR
MRPL36
BRD9
ZDHHC11
LPCAT1
CLPTM1L
NKD2
C5orf55
SLC6A19
SLC6A18
MIR4277
MIR4457
MIR4456

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p11.2.

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

Genes
EGFR
SNORA73\|ENSG00000252054.1
SEC61G

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q21.3.

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

Genes
ARNT
SNORA40\|ENSG00000253047.1
RN7SL600P
RN7SL473P
C1orf138
CTSK
CTSS
ENSA
MCL1
ADAMTSL4
GOLPH3L
HORMAD1
MIR4257

Genes in Wide Peak

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

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

Genes
LINC00393

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p21.1.

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

Genes
SNORA63\|ENSG00000199473.1
AHR
SNX13

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16p13.2.

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

Genes
C16orf72
RN7SL743P
ABAT
PMM2
USP7
CARHSP1
TMEM186
METTL22
TMEM114

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 22q12.2.

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

Genes
EWSR1
NF2
RNA5SP496
RN7SL633P
TUG1
MIR3200
SEC14L6
KIAA1658
MGC20647
RFPL1S
SNORD125
AP1B1
LIF
LIMK2
NEFH
OSM
RFPL1
SMTN
TCN2
NIPSNAP1
THOC5
MTMR3
GAL3ST1
SF3A1
RASL10A
GAS2L1
MORC2
PES1
SEC14L2
PATZ1
OSBP2
C22orf31
RHBDD3
INPP5J
UQCR10
PLA2G3
MTFP1
ZMAT5
TBC1D10A
KREMEN1
ZNRF3
ASCC2
RNF185
PIK3IP1
EMID1
HORMAD2
DUSP18
CABP7
RNF215
SEC14L3
SEC14L4
SLC35E4
CCDC157
GATSL3
MIR3928

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.33.

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

Genes
PIK3CA
BCL6
EIF4A2
ETV5
LPP
SOX2
TFRC
FAM157A
FYTTD1
snoU13\|ENSG00000238491.1
MIR4797
U4\|ENSG00000272359.1
RN7SL738P
RN7SL434P
UBXN7
SDHAP1
RN7SL773P
LINC00969
RNU6ATAC24P
RN7SL36P
MIR3137
LINC00884
LINC00887
RN7SL215P
RN7SL447P
snoU13\|ENSG00000238902.1
RN7SKP222
RN7SKP296
RN7SL486P
MIR944
MIR28
snoU13\|ENSG00000239093.1
RTP4
SNORA4\|ENSG00000263776.1
SNORA63\|ENSG00000200320.1
SNORA81\|ENSG00000221420.2
SNORA63\|ENSG00000200418.1
SNORD2\|ENSG00000238942.1
KNG1
CRYGS
RN7SL637P
TRA2B
MIR548AQ
SENP2
snoU13\|ENSG00000239146.1
SNORD66\|ENSG00000212158.1
MIR1224
CYP2AB1P
SNORA4\|ENSG00000251730.1
SNORA63\|ENSG00000199363.1
SNORA81\|ENSG00000253092.1
SNORA63\|ENSG00000201229.1
LINC00888
RNA5SP151
DCUN1D1
RN7SKP265
RNA5SP150
RN7SL703P
RN7SL229P
U8\|ENSG00000201810.1
RNA5SP149
snoU13\|ENSG00000239096.1
GNB4
SNORA25\|ENSG00000201957.1
RNA5SP148
SNORA18\|ENSG00000200288.1
RN7SKP52
LINC00578
LINC00501
RNA5SP147
snoU13\|ENSG00000271842.1
MIR4789
RN7SKP40
RN7SKP234
snoU13\|ENSG00000239141.1
SNORA72\|ENSG00000200355.1
RN7SL141P
PP13439
snoU13\|ENSG00000238359.1
MIR569
RNY5P3
CLDN11
TERC
EGFEM1P
RN7SKP298
MIR720
ACTL6A
AHSG
APOD
BCHE
BDH1
AP2M1
CLCN2
CPN2
DGKG
DLG1
DVL3
ECT2
EHHADH
EIF4G1
EPHB3
MECOM
FGF12
GHSR
GP5
HRG
HES1
IL1RAP
MFI2
MUC4
NDUFB5
OPA1
PAK2
PCYT1A
SERPINI1
SERPINI2
PLD1
POLR2H
PPP1R2
PRKCI
MASP1
PSMD2
RFC4
RPL35A
SI
ST6GAL1
SKIL
SLC2A2
SST
THPO
SEC62
FXR1
TP63
CHRD
TNFSF10
EIF2B5
USP13
CLDN1
MAP3K13
ADIPOQ
KIAA0226
ECE2
ABCC5
TNK2
ALG3
KCNMB2
IGF2BP2
CLDN16
PDCD10
SLITRK3
NLGN1
NCBP2
TNIK
MCF2L2
ATP11B
VPS8
ACAP2
GPR160
FETUB
LAMP3
KCNMB3
GOLIM4
ZNF639
PEX5L
DNAJB11
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MYNN
EIF5A2
MCCC1
HRASLS
MRPL47
NCEH1
SLC7A14
MAGEF1
ZMAT3
FNDC3B
ATP13A3
TBL1XR1
ZBBX
LRRC31
MAP6D1
PHC3
PIGZ
SPATA16
B3GNT5
IQCG
ATP13A4
ACTRT3
LRCH3
CEP19
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
CAMK2N2
TM4SF19
RPL39L
DNAJC19
FAM131A
ZDHHC19
LRRC15
FAM43A
TMEM207
RTP1
TTC14
WDR49
LRRC34
MB21D2
XXYLT1
CCDC50
PYDC2
RNF168
HTR3C
LIPH
HTR3D
RPL22L1
SLC51A
FBXO45
MUC20
SENP5
NAALADL2
TCTEX1D2
SMCO1
UTS2B
HTR3E
C3orf70
TPRG1
CCDC39
LRRIQ4
SAMD7
RTP2
OSTN
ATP13A5
WDR53
ANKRD18DP
NRROS
TMEM212
LINC00885
C3orf65
GMNC
MIR551B
MIR570
MIR922
MIR1263
MIR4448

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q23.3.

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

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

Genes in Wide Peak

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

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

Genes
FGFR3
LETM1
TACC3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q21.

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

Genes
C6orf203
PDSS2
BEND3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q13.3.

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

Genes
SNORA3\|ENSG00000221639.1
RNU6ATAC5P
RNU4ATAC9P
AFM
AFP
ALB
ANKRD17
RASSF6
COX18

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p25.1.

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

Genes
SNORA2\|ENSG00000206647.1
SNORA26\|ENSG00000212558.1
snoU13\|ENSG00000238462.1
IAH1
snoU13\|ENSG00000238888.1
MBOAT2
RNU6ATAC37P
RN7SKP112
FLJ30594
SNORA31\|ENSG00000252238.1
RN7SL531P
DCDC2C
SNORA73\|ENSG00000252531.1
snoU13\|ENSG00000238722.1
TMEM18
FAM110C
ACP1
ID2
RPS7
RRM2
SOX11
ADAM17
TPO
TSSC1
PXDN
KLF11
ASAP2
TAF1B
ITGB1BP1
RNF144A
YWHAQ
MYT1L
SH3YL1
GRHL1
TRAPPC12
CPSF3
SNTG2
ADI1
ALLC
KIDINS220
COLEC11
RSAD2
CMPK2
CYS1
RNASEH1
FAM150B
LINC00299
C2orf48
LINC00487
MIR4261

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q22.2.

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

Genes
BIRC3
MMP12
WTAPP1
BIRC2
MMP1
MMP3
MMP7
MMP8
MMP10
MMP13
MMP20
YAP1
MMP27
TMEM123

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p12.1.

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

Genes
KRAS
RN7SKP262
BCAT1
LRMP
RASSF8
CASC1
LYRM5
IFLTD1
C12orf77

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.43.

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

Genes
TFPT
ZNF331
RN7SL526P
ZNF417
ZNF814
ZNF134
ZNF548
ZNF805
ZNF264
DUXA
U3\|ENSG00000252683.1
MIMT1
SMIM17
ZNF71
ZSCAN5D
ZSCAN5C
RFPL4AL1
RN7SKP109
CCDC106
TMEM238
SYT5
snoU13\|ENSG00000239137.1
KIR3DX1
LILRA6
LENG1
NDUFA3
MIR935
MIR371B
RN7SL317P
ZNF813
ZNF761
FAM90A28P
FAM90A27P
ZNF321P
ZNF888
ZNF600
FCAR
IL11
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
LAIR1
LAIR2
CNOT3
PEG3
PRKCG
PTPRH
RPL28
RPS9
AURKC
TNNI3
TNNT1
ZNF17
ZNF28
ZNF135
ZNF154
NCR1
ZNF256
LILRB2
ZNF211
TRAPPC2P1
ZNF460
LILRB1
LILRB5
LILRB4
LILRA1
LILRB3
LILRA3
LILRA2
U2AF2
PPP6R1
LILRA4
ZIM2
HSPBP1
PRPF31
UBE2S
EPN1
ZNF580
GP6
ZNF581
PPP1R12C
ZNF586
EPS8L1
ZNF444
NLRP2
ZNF416
ZNF415
NAT14
VN1R1
ZNF304
TTYH1
ZNF471
USP29
CACNG8
CACNG7
CACNG6
ZNF667
ZSCAN18
TSEN34
MBOAT7
ZSCAN5A
ZNF329
ZNF419
ISOC2
ZNF665
ZNF552
ZNF671
ZNF702P
ZNF606
ZNF611
BRSK1
ZNF347
SUV420H2
ZNF587
FIZ1
GALP
ZNF628
ZNF551
ZNF468
ZNF160
ZNF835
ZNF765
NLRP12
MYADM
ZNF845
LENG9
BIRC8
RDH13
ZIM3
LENG8
KIR3DL3
ZNF816
ZNF543
COX6B2
OSCAR
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
C19orf18
ZNF418
TMEM190
TMC4
TPM3P9
ZNF524
ZNF784
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF320
ZNF550
ZNF579
ZNF525
NLRP7
ZSCAN4
NLRP11
TMEM86B
ZNF549
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
VSTM1
TMEM150B
FAM71E2
VN1R2
VN1R4
NLRP9
ZNF677
RFPL4A
ZSCAN5B
ZNF530
DNAAF3
LILRA5
ZNF773
ZNF470
ZNF749
ZNF772
TARM1
MIR371A
MIR372
MIR373
DPRX
MIR498
MIR520E
MIR519E
MIR520F
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
SBK2
SHISA7
SGK110
ZNF587B
MIR1323
ZNF865
MIR4752

Genes in Wide Peak

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

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

Genes
CBFB
CDH1
NPIPB15
HCCAT5
PKD1L3
IST1
SNORD71
SNORA70D
TAT
SNORD112\|ENSG00000251700.1
RNU6ATAC25P
FLJ00418
SNORD111\|ENSG00000221066.1
SNORD111B
SF3B3
RN7SL279P
RN7SL407P
snoU13\|ENSG00000238734.1
FKSG63
PDXDC2P
MIR140
SNORA62\|ENSG00000252443.1
snoU13\|ENSG00000238683.1
COG8
CHTF8
RPS2P45
RNA5SP429
snoU109\|ENSG00000252640.1
snoU109\|ENSG00000252040.1
snoU13\|ENSG00000238343.1
SLC7A6OS
SNORA48\|ENSG00000212445.1
CTRL
NUTF2
RN7SKP118
TRADD
AARS
AP1G1
AGRP
ZFHX3
CALB2
CDH3
DHODH
NQO1
E2F4
HAS3
HP
HPR
HSD11B2
HSF4
LCAT
NFATC3
PSKH1
PSMB10
PSMD7
ST3GAL2
SLC9A5
SLC12A4
SNTB2
TERF2
ZNF19
ZNF23
NOL3
SLC7A6
ATP6V0D1
DHX38
CHST4
CTCF
NFAT5
WWP2
DDX19B
PHLPP2
EDC4
PLA2G15
COG4
PLEKHG4
LRRC29
VPS4A
NOB1
TMEM208
FHOD1
ZDHHC1
PARD6A
NIP7
TPPP3
PRMT7
HYDIN
DUS2L
CHTF8
TXNL4B
PDPR
LRRC36
DDX19A
FBXL8
SMPD3
ZNF821
VAC14
FTSJD1
DDX28
TSNAXIP1
THAP11
RANBP10
PDF
DPEP2
DPEP3
ACD
FAM65A
TANGO6
ELMO3
ESRP2
CENPT
C16orf70
CYB5B
GFOD2
PMFBP1
ENKD1
B3GNT9
CIRH1A
MARVELD3
MTSS1L
EXOSC6
NRN1L
ZFP90
RLTPR
KCTD19
IL34
TMED6
FUK
EXOC3L1
CLEC18C
ATXN1L
CLEC18A
C16orf86
C16orf47
MIR328
CLEC18B
KIAA0895L
MIR1538

Genes in Wide Peak

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

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

Genes
JAK2
CD274
RN7SL5P
SNORD27\|ENSG00000251699.1
RN7SL123P
snoU13\|ENSG00000252110.1
RN7SL25P
C9orf38
MLANA
snoU13\|ENSG00000238654.1
INSL4
AK3
CDC37L1
CARM1P1
RN7SL592P
RNA5SP279
DMRT1
GLDC
PTPRD
RFX3
RLN1
RLN2
SLC1A1
SMARCA2
VLDLR
KIAA0020
RCL1
DMRT2
INSL6
KDM4C
RANBP6
SPATA6L
PLGRKT
KIAA1432
DMRT3
ERMP1
PDCD1LG2
TPD52L3
IL33
C9orf123
UHRF2
KIAA2026
KCNV2
GLIS3
PPAPDC2
MIR4665

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q23.3.

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

Genes
MYB
AHI1
MIR548A2

Genes in Wide Peak

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

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

Genes
LMO2
MIR1343
EHF
CD59
C11orf91
CAT
CD44
ELF5
CAPRIN1
SLC1A2
PDHX
KIAA1549L
ABTB2
FBXO3
APIP
NAT10

Genes in Wide Peak

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

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

Genes
snoU13\|ENSG00000238714.1
SNORD112\|ENSG00000238966.1
RN7SL149P
MIR486
ANK1
IKBKB
PLAT
KAT6A
AP3M2

Genes in Wide Peak

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

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

Genes
MYC
RN7SKP226
TMEM75
POU5F1B
CASC8
CCAT1
PCAT2
PCAT1
FAM84B
MIR1205
MIR1207
PVT1
MIR1208

Genes in Wide Peak

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

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

Genes
SNX29P2
SNX29P2
RRN3P2
snoU13\|ENSG00000238699.1
MIR4517
SNORA43\|ENSG00000252461.1
MIR4721
snoU13\|ENSG00000238352.1
NPIPB9
snoU13\|ENSG00000238684.1
NPIPB8
ATP2A1
CD19
SULT1A2
SULT1A1
TUFM
EIF3C
ATXN2L
SH2B1
LAT
RABEP2
SPNS1
NFATC2IP
NPIPB11

Genes in Wide Peak

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

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

Genes
MIR4523
TIAF1
NEK8
CRYBA1
FLOT2
TRAF4
ERAL1
GIT1
PIPOX
FAM222B
NUFIP2
TAOK1
PHF12
TP53I13
ABHD15
SEZ6
ANKRD13B
DHRS13
MYO18A
MIR4523
MIR4732

Genes in Wide Peak

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

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

Genes
MTND1P15
UBBP4
RN7SL426P
TMEM11
KCNJ12
MAP2K3
USP22
DHRS7B
C17orf103
FAM27L
CCDC144NL
C17orf51
MTRNR2L1

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 - 36 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
9p21.3	6.9584e-213	1.7566e-203	chr9:21931610-22003135	2
13q14.2	7.568e-34	8.0418e-34	chr13:48875329-49563699	5
5q12.1	1.2146e-33	1.2172e-33	chr5:58998410-59780946	2
4q22.1	2.932e-29	1.3895e-25	chr4:91271445-93240505	1
2q37.1	2.0711e-36	2.4681e-18	chr2:227663186-243199373	169
16p13.3	3.2014e-16	3.2014e-16	chr16:3675448-4004422	2
2q22.1	1.2352e-21	5.9003e-15	chr2:140708948-143637838	2
3p14.2	9.7528e-15	9.7528e-15	chr3:59034763-61547330	3
16q23.1	6.1536e-14	6.1536e-14	chr16:78098006-79031486	1
10q23.31	1.7533e-10	1.785e-10	chr10:89617158-90034038	3
14q24.1	1.3074e-08	1.2604e-08	chr14:68275375-69288431	4
6p25.3	1.8517e-08	1.9349e-08	chr6:1-2624052	10
4q34.2	3.0518e-13	6.0848e-08	chr4:170674827-191154276	96
19p13.3	7.2756e-08	7.4896e-08	chr19:1-1867911	73
11p15.5	2.9151e-06	2.9151e-06	chr11:516521-748945	14
8p23.3	6.7754e-08	1.7517e-05	chr8:1-10530153	72
18q23	2.627e-05	2.6067e-05	chr18:60983938-78077248	64
17p12	3.4897e-05	3.569e-05	chr17:14111288-16121163	23
22q13.32	4.8268e-05	5.0391e-05	chr22:47571204-51304566	43
2q34	6.0232e-25	0.000108	chr2:211542637-214176087	4
15q13.1	0.00034787	0.00034203	chr15:23689595-32934882	78
1p36.11	0.00052598	0.00052598	chr1:26963410-27155421	5
9p23	9.9535e-17	0.002361	chr9:7887952-12687261	3
Xp11.3	0.0047013	0.0046243	chrX:44702452-45008304	2
6q21	3.4915e-05	0.0069405	chr6:67919847-125441515	271
11q23.3	8.8603e-05	0.025277	chr11:102825636-133308731	293
1q32.1	0.033566	0.033566	chr1:188124783-233120332	389
6q27	0.00027473	0.039299	chr6:148058540-171115067	145
Xq21.33	0.042298	0.042383	chrX:95661798-99356556	5
12p13.1	0.05664	0.057264	chr12:10607226-13714180	51
7q36.3	0.062073	0.062758	chr7:151211607-159138663	39
8p21.3	4.5185e-08	0.07604	chr8:4985853-36623303	252
9q22.33	0.11788	0.11548	chr9:91360187-115924931	198
11q25	0.00015732	0.12912	chr11:102700695-135006516	308
10p11.21	0.16614	0.16327	chr10:16858758-38300099	127
12q24.33	0.22328	0.21865	chr12:127253242-133851895	50

Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q14.2.

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

Genes
RB1
LINC00462
RCBTB2
LPAR6
CYSLTR2

Genes in Wide Peak

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

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

Genes
FKSG52
MIR582

Genes in Wide Peak

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

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

Genes
RN7SKP248

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q37.1.

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

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

Genes in Wide Peak

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

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

Genes
CREBBP
TRAP1

Genes in Wide Peak

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

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

Genes
RN7SL283P
LRP1B

Genes in Wide Peak

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

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

Genes
FHIT
U3\|ENSG00000212211.1
NPCDR1

Genes in Wide Peak

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

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

Genes
PIH1

Genes in Wide Peak

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

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

Genes
PTEN
SNORD74\|ENSG00000200891.1
KLLN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q24.1.

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

Genes
RN7SL108P
RN7SL706P
ZFP36L1
RAD51B

Genes in Wide Peak

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

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

Genes
IRF4
RN7SL352P
snoU13\|ENSG00000238438.1
FOXF2
FOXC1
GMDS
EXOC2
DUSP22
FOXQ1
HUS1B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q34.2.

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

Genes
DUX4
RNA5SP175
RNA5SP174
HSP90AA4P
CYP4V2
SNORA31\|ENSG00000253013.1
TLR3
snoU13\|ENSG00000239034.1
PDLIM3
UFSP2
SNORD79
RN7SL28P
snoU13\|ENSG00000239116.1
snoU13\|ENSG00000238596.1
snoU13\|ENSG00000238319.1
U3\|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65\|ENSG00000212191.1
RNA5SP173
snoU13\|ENSG00000252388.1
RNA5SP172
RN7SKP136
SNORA51\|ENSG00000201516.1
SCRG1
HMGB2
MIR548T
RN7SL253P
RNU6ATAC13P
HSP90AA6P
AGA
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
GPM6A
HPGD
ING2
IRF2
KLKB1
MTNR1A
VEGFC
GLRA3
SORBS2
SAP30
HAND2
MFAP3L
ADAM29
FAM149A
FBXO8
AADAT
GALNT7
CLDN22
NEIL3
CDKN2AIP
TENM3
LRP2BP
STOX2
KIAA1430
SPCS3
TRAPPC11
MLF1IP
WWC2
CEP44
SNX25
WDR17
ZFP42
SPATA4
ENPP6
ASB5
RWDD4
CCDC111
TRIML2
CCDC110
TRIML1
ANKRD37
HELT
C4orf47
DUX4L4
GALNTL6
FRG2
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
CLDN24
MIR1305
MIR4276
MIR3945
MIR4455

Genes in Wide Peak

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

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

Genes
STK11
TCF3
FSTL3
MIR1909
ONECUT3
UQCR11
RN7SL477P
NDUFS7
C19orf24
POLR2E
ARID3A
CFD
MIR4745
RNA5SP462
OR4F17
FAM138F
WASH5P
ATP5D
AZU1
HCN2
BSG
CDC34
CIRBP
CNN2
EFNA2
ELANE
GAMT
GPX4
GZMM
PALM
POLRMT
PRTN3
PTBP1
RPS15
MADCAM1
PPAP2C
MED16
APC2
ABCA7
UQCR11
SBNO2
HMHA1
SHC2
DAZAP1
FGF22
THEG
MBD3
MIER2
PCSK4
RNF126
WDR18
REXO1
LPPR3
KLF16
KISS1R
MUM1
MIDN
R3HDM4
TMEM259
TPGS1
REEP6
GRIN3B
MISP
PLK5
C2CD4C
C19orf25
ATP8B3
C19orf26
ODF3L2
ADAMTSL5
MEX3D
PRSS57
MIR3187

Genes in Wide Peak

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

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

Genes
HRAS
TMEM80
SCT
MIR210HG
DRD4
IRF7
RASSF7
DEAF1
CDHR5
PHRF1
EPS8L2
LRRC56
C11orf35
MIR210

Genes in Wide Peak

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

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

Genes
PRSS51
snoU13\|ENSG00000238496.1
snoU13\|ENSG00000239065.1
MIR597
U3\|ENSG00000252543.1
SNORA70\|ENSG00000207244.1
RN7SL178P
SGK223
ALG1L13P
FAM86B3P
LRLE1
FAM85B
FAM90A24P
FAM66E
DEFB105A
DEFB105B
DEFB103B
ZNF705G
FAM66B
XKR5
MIR4659A
AGPAT5
RN7SKP159
RN7SL318P
SNORA70\|ENSG00000206661.1
RN7SL872P
RNA5SP251
RPL23AP53
OR4F21
ANGPT2
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
CLN8
MSRA
TNKS
MYOM2
DLGAP2
MFHAS1
ARHGEF10
KBTBD11
SPAG11B
FBXO25
CSMD1
MCPH1
PPP1R3B
ERI1
CLDN23
DEFB104A
TDRP
ERICH1
ZNF596
PRSS55
DEFB106A
DEFB107A
LINC00599
DEFB103A
DEFB107B
DEFB104B
DEFB106B
SPAG11A
MIR596
DEFA1B
ZNF705B
DEFB4B
MIR548I3
MIR4286
MIR4660

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q23.

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

Genes
RBFA
RBFADN
SALL3
RNA5SP461
SNORA25\|ENSG00000199392.1
GALR1
LINC00683
ZNF516
SMIM21
ZADH2
RN7SL551P
RN7SL401P
MIR548AV
RNA5SP460
RN7SL795P
CDH7
CYB5A
KDSR
MBP
NFATC1
SERPINB2
SERPINB5
SERPINB8
SERPINB10
SERPINB13
SERPINB3
SERPINB4
ZNF236
SERPINB7
CTDP1
SOCS6
VPS4B
TSHZ1
CD226
TXNL4A
ADNP2
RTTN
KCNG2
CDH19
TIMM21
TMX3
ZNF407
CNDP2
CCDC102B
PQLC1
NETO1
PARD6G
CNDP1
SERPINB12
SERPINB11
DSEL
FAM69C
CBLN2
FBXO15
GTSCR1
DOK6
LINC00305
LINC00908
HMSD
ATP9B
LINC00909
HSBP1L1
C18orf63
MIR5011

Genes in Wide Peak

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

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

Genes
RN7SL442P
RNA5SP436
ZNF286A
SNORA74\|ENSG00000252129.1
CDRT1
RN7SL792P
MIR4731
snoU13\|ENSG00000238806.1
CDRT8
CDRT7
HS3ST3B1
CDRT15
ADORA2B
PMP22
TRIM16
TTC19
ZNF286A
TEKT3
ZSWIM7
TVP23C
CDRT4
TBC1D26
CDRT1

Genes in Wide Peak

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

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

Genes
ARSA
RN7SL500P
DENND6B
TTLL8
ALG12
RN7SKP252
ACR
CHKB
CPT1B
TYMP
MAPK11
MAPK12
SBF1
PPP6R2
ZBED4
SCO2
RABL2B
MLC1
MAPK8IP2
PLXNB2
BRD1
FAM19A5
NCAPH2
MOV10L1
MIOX
PANX2
CRELD2
ADM2
TRABD
HDAC10
SHANK3
TUBGCP6
LMF2
KLHDC7B
C22orf34
LINC00898
IL17REL
PIM3
ODF3B
SYCE3
MIR3201
MIR3667
MIR4535

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q34.

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

Genes
MIR548F2
RNA5SP119
ERBB4
IKZF2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q13.1.

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

Genes
RN7SL286P
RN7SL539P
GOLGA8O
U8\|ENSG00000206987.1
ULK4P1
RN7SL185P
GOLGA8K
CHRNA7
SNORA18\|ENSG00000206849.1
MIR211
RN7SL82P
U8\|ENSG00000252602.1
RN7SL628P
GOLGA8H
U8\|ENSG00000207430.1
ULK4P2
RN7SL796P
GOLGA8Q
RN7SL196P
GOLGA8R
U8\|ENSG00000238519.1
RN7SL469P
GOLGA8T
U8\|ENSG00000207432.1
ULK4P3
RN7SL673P
GOLGA8J
snoZ278
GOLGA6L7P
WHAMMP2
RN7SL719P
GOLGA8M
RN7SL829P
RN7SL238P
GOLGA8F
RNA5SP391
LINC00929
SNORA48\|ENSG00000212604.1
MIR4715
RNA5SP390
ATP10A
SNORD109B
SNORD115\|ENSG00000212428.1
SNORD109A
SNORD108
SNORD64\|ENSG00000270704.2
SNHG14
SNURF
snoU13\|ENSG00000238615.1
PWRN1
PWRN2
MAGEL2
APBA2
GABRA5
GABRB3
GABRG3
TRPM1
NDN
OCA2
SNRPN
TJP1
UBE3A
MKRN3
HERC2
ARHGAP11A
FAN1
FAM189A1
NPAP1
KLF13
MTMR10
NDNL2
CHRFAM7A
ARHGAP11B
OTUD7A
GOLGA8G
HERC2P9
GOLGA8N
MIR4508

Genes in Wide Peak

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

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

Genes
ARID1A
RN7SL165P
RN7SL501P
snoU13\|ENSG00000238316.1
PIGV

Genes in Wide Peak

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

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

Genes
RN7SL5P
SNORD27\|ENSG00000251699.1
PTPRD

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp11.3.

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

Genes
KDM6A
DUSP21

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q21.

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

Genes
PRDM1
ROS1
GOPC
CLVS2
RN7SL564P
SIGLECP3
RNA5SP215
MIR548B
RN7SKP51
RN7SKP18
RNA5SP214
FAM26E
TSPYL1
NT5DC1
FRK
RNA5SP213
snoU13\|ENSG00000238563.1
U3\|ENSG00000253091.1
snoU13\|ENSG00000239095.1
snoU13\|ENSG00000239015.1
C6orf3
KIAA1919
RPF2
snoU13\|ENSG00000238775.1
SNORA40\|ENSG00000212587.1
RN7SL617P
snoU13\|ENSG00000238474.1
CCDC162P
C6orf183
ZNF259P1
LINC00222
RNA5SP212
snoU13\|ENSG00000238974.1
SNORA73\|ENSG00000253090.1
SCML4
RTN4IP1
RNA5SP211
RN7SL47P
RN7SKP211
POPDC3
LINC00577
SNORA33\|ENSG00000202283.1
snoU13\|ENSG00000238999.1
PRDM13
TSTD3
RN7SL509P
RN7SL797P
SNORA18\|ENSG00000252249.1
U3\|ENSG00000221455.1
U3\|ENSG00000200492.1
RN7SL415P
RN7SKP110
CASP8AP2
snoU13\|ENSG00000238747.1
RN7SL11P
RN7SL336P
SNORA73\|ENSG00000222145.1
RN7SL183P
snoU13\|ENSG00000238628.1
C6ORF165
RN7SKP209
RN7SL643P
SNHG5
CYB5R4
RWDD2A
SNORA70\|ENSG00000206886.1
RNA5SP210
SNORD112\|ENSG00000252932.1
HTR1B
U6\|ENSG00000272445.1
snoU13\|ENSG00000239132.1
RNA5SP209
RN7SKP163
U3\|ENSG00000221332.1
MB21D1
snoU13\|ENSG00000238464.1
OOEP
OGFRL1
U3\|ENSG00000221345.1
B3GAT2
C6orf57
COL19A1
RNA5SP208
SNORD65\|ENSG00000212229.1
AIM1
AMD1
BAI3
BCKDHB
CCNC
CGA
CNR1
COL9A1
COL10A1
COL12A1
COX7A2
EEF1A1
EPHA7
FABP7
FOXO3
FYN
GABRR1
GABRR2
GJA1
GPR6
GRIK2
HDAC2
HSF2
HTR1E
IMPG1
KPNA5
LAMA4
MARCKS
MAN1A1
ME1
MYO6
NT5E
PGM3
PLN
POU3F2
PREP
PKIB
REV3L
SIM1
SMPD2
ELOVL4
MAP3K7
NR2E1
TPBG
TTK
DDO
SNX3
RNGTT
CD164
WISP3
WASF1
TBX18
HMGN3
FHL5
ATG5
ZBTB24
SNAP91
FIG4
TRDN
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
SMPDL3A
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
MDN1
TSPYL4
UFL1
ORC3
MTO1
ASF1A
PNISR
IBTK
SENP6
FBXL4
SLC17A5
FILIP1
SESN1
OSTM1
NDUFAF4
DSE
TUBE1
C6orf203
CDC40
RWDD1
UBE2J1
COQ3
PHIP
SOBP
AKIRIN2
QRSL1
DDX43
FAM46A
TMEM30A
LMBRD1
KCNQ5
RARS2
PDSS2
SMIM8
LYRM2
SNX14
SERINC1
HACE1
FAM135A
BEND3
RRAGD
BACH2
SMAP1
C6orf164
MICAL1
FAM184A
MANEA
LINC00472
KHDC1
GPR63
SPACA1
SH3BGRL2
ARMC2
MCHR2
FAXC
GJA10
USP45
SLC22A16
UBE3D
GTF3C6
MRAP2
KLHL32
NUS1
SLC16A10
RIPPLY2
IRAK1BP1
CD109
PM20D2
SRSF12
RNF217
NKAIN2
KHDC3L
C6orf165
PRSS35
LCA5
C6orf163
AK9
FAM26D
ZUFSP
FAM162B
TBC1D32
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
MMS22L
MCM9
CEP57L1
PPIL6
DCBLD1
DPPA5
RSPH4A
GJB7
CEP85L
LIN28B
MIR30A
MIR30C2
FAM26F
RFPL4B
FAM229B
MIR587
METTL24
TRAPPC3L
KHDC1L
MIR2113
MIR3144
MIR4282
MIR4464
MIR4643
MIR548AI
MIR4463

Genes in Wide Peak

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

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

Genes
DDX6
PCSK7
SDHD
ATM
CBL
DDX10
FLI1
PAFAH1B2
POU2AF1
SDHD
ARHGEF12
snoU13\|ENSG00000238693.1
RNU6ATAC12P
RN7SL167P
LINC00167
KCNJ5
RN7SKP279
RN7SKP121
MIR3167
snoU13\|ENSG00000238855.1
RN7SL351P
KRT18P59
SLC37A2
RNA5SP352
TBRG1
OR10D3
U8\|ENSG00000200496.1
SNORD14C
SNORD14D
SNORD14E
snoU13\|ENSG00000239079.1
RNU4ATAC5P
RNU4ATAC10P
SC5D
TBCEL
OAF
THY1
MFRP
ACA64\|ENSG00000252119.1
HINFP
C2CD2L
MIR3656
RPS25
RN7SL529P
RN7SL688P
BCL9L
CXCR5
TTC36
RN7SL86P
CD3G
MPZL3
TMPRSS4
SCARNA11\|ENSG00000252992.1
RNY4P6
ZNF259
snoU13\|ENSG00000238625.1
LINC00900
snoU13\|ENSG00000239153.1
ACA59\|ENSG00000252870.1
snoU13\|ENSG00000238724.1
ATF4P4
snosnR66
C11orf34
RNA5SP351
HSPB2
ALG9
ALG9
RN7SKP273
SIK2
RNA5SP350
SNORD39\|ENSG00000264997.1
RNA5SP349
RNA5SP348
ACAT1
ACRV1
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CASP1
CASP4
CASP5
CD3D
CD3E
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HTR3A
IL10RA
IL18
STT3A
KCNJ1
VWA5A
MCAM
KMT2A
NCAM1
NFRKB
NNMT
NPAT
NRGN
PPP2R1B
PTS
PVRL1
RDX
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
UPK2
ZBTB16
ZNF202
CUL5
BARX2
USP2
HTR3B
ZW10
UBE4A
EI24
FEZ1
ARHGAP32
RBM7
MPZL2
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
EXPH5
PHLDB1
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
REXO2
OR8B8
TIMM8B
OR8B2
DCPS
ZBTB44
DDX25
NTM
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
NXPE4
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
IFT46
PRDM10
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
TP53AIP1
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
DYNC2H1
NLRX1
MSANTD2
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
BCO2
TMPRSS13
DCUN1D5
MSANTD4
KIRREL3
BUD13
TMEM25
RPUSD4
UBASH3B
DIXDC1
ZC3H12C
ESAM
ALKBH8
FDXACB1
C11orf52
TIRAP
CARD16
C1QTNF5
PANX3
APOA5
TMEM45B
C11orf93
PIH1D2
NXPE1
NXPE2
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
PATE1
C11orf65
ADAMTS15
C11orf45
HYLS1
TMEM218
OR8B12
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TMEM136
HEPACAM
ANKK1
RNF214
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
C11orf44
CCDC84
TMEM225
OR8D4
C11orf53
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
PATE2
PATE4
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
HEPN1
CLDN25
PATE3
MIR4301
CASP12
MIR4493
MIR4491
MIR4492
MIR4693

Genes in Wide Peak

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

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

Genes
ELK4
MDM4
SLC45A3
NTPCR
RN7SL299P
LINC00582
TRAX
RNA5SP80
MIR1182
snoU13\|ENSG00000238985.1
RN7SL837P
RNA5SP79
RN7SL467P
RNA5SP78
RN7SKP276
TMEM78
SNORA51\|ENSG00000206878.1
RNA5SP18
RNA5S17
RNA5S16
RNA5S15
RNA5S14
RNA5S13
RNA5S12
RNA5S11
RNA5S10
RNA5S9
RNA5S8
RNA5S7
RNA5S6
RNA5S5
RNA5S4
RNA5S3
RNA5S2
RNA5S1
RNA5SP19
BTNL10
RNF187
MIR3620
MIR5008
WNT9A
ZNF678
RNA5SP77
RN7SKP165
snoU13\|ENSG00000239094.1
snoU13\|ENSG00000238545.1
MIR4742
snoU13\|ENSG00000238856.1
MIR320B2
SNORA72\|ENSG00000201898.1
RN7SKP49
CAPN8
snoU13\|ENSG00000239054.1
RN7SL276P
HLX
RNU6ATAC35P
HDAC1P2
RN7SL464P
SNORA36B
snoU13\|ENSG00000238576.1
snoU13\|ENSG00000238798.1
U3\|ENSG00000221673.1
RNA5SP76
SLC30A10
U3\|ENSG00000212610.1
C1orf143
LINC00210
SPATA17
SNORD116\|ENSG00000202498.1
RN7SL512P
SNORA16B
RN7SKP98
MIR3122
SNORA26\|ENSG00000212187.1
RN7SL344P
SLC30A1
KCNH1
SERTAD4
MIR4260
MIR205HG
MIR29B2
MIR29C
snoU13\|ENSG00000238401.1
FAIM3
IL20
SNORD112\|ENSG00000252853.1
C1orf147
SRGAP2
SNORD60\|ENSG00000252692.1
C1orf186
AVPR1B
FAM72A
SNORA72\|ENSG00000201944.1
SNORD112\|ENSG00000252946.1
SCARNA20\|ENSG00000251861.1
RNA5SP75
RNA5SP74
SNRPE
ZBED6
SNORA77\|ENSG00000221643.1
RABIF
PCAT6
SNORA70\|ENSG00000253042.1
U6\|ENSG00000272262.1
snoU13\|ENSG00000239046.1
snoU13\|ENSG00000238571.1
PTPRVP
GPR37L1
SNORA70\|ENSG00000206637.1
MIR1231
MIR5191
RPS10P7
ASCL5
LINC00862
MIR181A1HG
MIR4735
U3\|ENSG00000252241.1
MIR1278
snoU109\|ENSG00000238754.1
RN7SKP126
RNA5SP73
RN7SKP156
ACTA1
ADORA1
PARP1
AGT
ARF1
ATF3
ATP2B4
C4BPA
C4BPB
CACNA1S
CAPN2
CD34
CENPF
CHI3L1
CHIT1
CR1
CR1L
CR2
CSRP1
CTSE
CD55
EIF2D
ELF3
EPHX1
EPRS
ESRRG
F13B
FMOD
NR5A2
GALNT2
GPR25
GUK1
H3F3A
CFH
CFHR1
CFHR2
HSD11B1
IL10
IRF6
ITPKB
KCNK2
KISS1
LAD1
LAMB3
LBR
MARK1
CD46
MYBPH
MYOG
PPP1R12B
NEK2
NVL
CDK18
PFKFB2
PIGR
PIK3C2B
PKP1
PLXNA2
PPP2R5A
PRELP
PROX1
PSEN2
PTPN7
PTPN14
PTPRC
RAB4A
RBBP5
REN
RGS1
RGS2
RGS13
RNPEP
SRP9
TROVE2
CNTN2
TGFB2
LEFTY2
TLR5
TNNI1
TNNT2
TP53BP2
TRAF5
TSNAX
USH2A
BTG2
HIST3H3
GNPAT
DYRK3
CDC42BPA
PPFIA4
DEGS1
B3GALT2
RAB7L1
TAF1A
MAPKAPK2
SOX13
IKBKE
TMEM63A
URB2
ZC3H11A
TMCC2
LPGAT1
KIF14
BPNT1
TIMM17A
LRRN2
LEFTY1
SPHAR
CAPN9
KDM5B
CFHR4
CFHR3
IL24
DUSP10
COG2
PLEKHA6
KIF21B
NFASC
FBXO28
CAMSAP2
CRB1
ABCB10
ZNF281
PHLDA3
DSTYK
RAB3GAP2
LMOD1
INTS7
NSL1
OPTC
RPS6KC1
DIEXF
TAF5L
DISC1
FLVCR1
UBE2T
CNIH4
PYCR2
NENF
IL19
G0S2
RRP15
GLRX2
ADIPOR1
TRIM17
KCTD3
UCHL5
DTL
CYB5R1
EGLN1
MAP10
LAX1
MARC2
SUSD4
GPATCH2
KLHDC8A
ETNK2
TMEM206
YOD1
BATF3
IARS2
IPO9
HHAT
ENAH
NUP133
RCOR3
C1orf106
SMYD2
LHX9
ADCK3
GJC2
CAMK1G
SIPA1L2
RHOU
KLHL12
LGR6
RGS18
NUCKS1
ACBD3
MARC1
ARV1
AIDA
JMJD4
C1orf116
C1orf35
TTC13
CDC73
PGBD5
C1orf115
HHIPL2
VASH2
WDR26
TRAF3IP3
CFHR5
TRIM11
NUAK2
DDX59
RASSF5
MIXL1
SPRTN
FCAMR
OBSCN
LINC00467
C1orf198
PPP1R15B
DISP1
WNT3A
NAV1
ANGEL2
IGFN1
TMEM183A
HIST3H2A
LEMD1
SLC26A9
SNAP47
CCSAP
LYPLAL1
ATP6V1G3
DNAH14
ARL8A
SYT2
GOLT1A
C1orf131
MRPL55
HIST3H2BB
TATDN3
NEK7
C1orf74
BROX
MFSD4
PM20D1
CNIH3
SHISA4
EXOC8
C1orf227
FAM71A
DENND1B
SDE2
C1orf65
IBA57
TMEM9
SLC41A1
SYT14
ASPM
LINC00303
LIN9
FAM5C
PRSS38
RD3
KCNT2
ZBTB41
MIA3
C1orf95
FAM89A
C1orf53
TMEM81
FAM177B
MIR181B1
MIR181A1
MIR215
C1orf132
RGS21
TRIM67
MIR135B
C1orf145
C1orf148
MIR4666A

Genes in Wide Peak

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

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

Genes
FGFR1OP
MLLT4
MIR4644
TCP10
TTLL2
GPR31
MIR1913
SFT2D1
SNORD45\|ENSG00000231297.2
LINC00473
SDIM1
RNA5SP226
RN7SL366P
CAHM
snoU13\|ENSG00000239136.1
AIRN
SNORA29
SNORA20\|ENSG00000207392.1
RNU4ATAC18P
C6orf99
RN7SL173P
MIR3692
snoU13\|ENSG00000252609.1
SNORD28\|ENSG00000212295.1
TFB1M
U8\|ENSG00000238963.1
CNKSR3
RNA5SP225
RNA5SP224
RNA5SP223
snoU13\|ENSG00000238939.1
RN7SKP268
RNY4P20
snoU13\|ENSG00000238594.1
RAET1K
SNORA2\|ENSG00000202343.1
GINM1
ZC3H12D
RN7SL234P
ACAT2
CCR6
ESR1
IGF2R
KIF25
LPA
MAS1
MAP3K4
OPRM1
PARK2
PCMT1
PDCD2
PLG
PSMB1
RPS6KA2
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCP1
TCTE3
DYNLT1
THBS2
EZR
VIP
RNASET2
SYNJ2
LATS1
QKI
WTAP
AKAP12
UST
PDE10A
KATNA1
SCAF8
TAB2
SASH1
SYNE1
MTHFD1L
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
DLL1
MRPL18
CLDN20
NOX3
SNX9
MPC1
UNC93A
MTRF1L
RMND1
PHF10
C6orf70
AGPAT4
TULP4
PLEKHG1
ARID1B
TMEM181
ZBTB2
SMOC2
ULBP3
C6orf211
ZDHHC14
FRMD1
LINC00574
CCDC170
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
RSPH3
FAM120B
FNDC1
LRP11
SERAC1
PPIL4
SYTL3
TAGAP
PACRG
RAET1E
RAET1L
PNLDC1
DACT2
C6orf118
OSTCP1
WDR27
PRR18
NUP43
RAET1G
SUMO4
C6orf120
IYD
TCP10L2
LINC00242
GTF2H5
TMEM242
MIR1202
MIR1273C
MIR3918
MIR3939
MIR4466

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq21.33.

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

Genes
SNORA25\|ENSG00000252296.1
RN7SL74P
RN7SKP194
DIAPH2
RPA4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.1.

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

Genes
ETV6
RNA5SP353
HTR7P1
SNORD88
GPRC5A
MIR613
DUSP16
LOH12CR2
TAS2R30
TAS2R64P
TAS2R20
TAS2R14
PRH2
TAS2R8
MAGOHB
EIF2S3L
CDKN1B
CREBL2
EMP1
GPR19
LRP6
PRB1
PRB3
PRB4
PRH1
YBX3
KLRAP1
PRR4
TAS2R9
TAS2R7
TAS2R13
TAS2R10
HEBP1
DDX47
MANSC1
STYK1
GPRC5D
KIAA1467
BCL2L14
APOLD1
GSG1
LOH12CR1
TAS2R43
TAS2R31
TAS2R46
TAS2R19
TAS2R50
C12orf36
TAS2R42
PRB2
MIR614

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q36.3.

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

Genes
LINC00689
MIR595
RN7SL142P
SHH
RN7SKP280
HTR5A
RN7SL845P
RN7SL811P
SNORA26\|ENSG00000212590.1
snoU13\|ENSG00000238557.1
RNA5SP250
FABP5P3
snoU13\|ENSG00000239045.1
DPP6
EN2
MNX1
INSIG1
PTPRN2
VIPR2
XRCC2
UBE3C
DNAJB6
PAXIP1
PRKAG2
NCAPG2
WDR60
ACTR3B
ESYT2
KMT2C
GALNT11
LMBR1
NOM1
C7orf13
RNF32
RBM33
GALNTL5
CNPY1
BLACE
MIR5707

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p21.3.

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

Genes
PCM1
WRN
RNA5SP264
RN7SKP201
RN7SL457P
RN7SL621P
SNORA70\|ENSG00000252505.1
SNORD13
RNA5SP263
RNA5SP262
RNA5SP261
UBXN8
TUBBP1
FAM183CP
LINC00589
RN7SL781P
RNA5SP260
RNA5SP259
MIR4287
snoU13\|ENSG00000238624.1
SDAD1P1
RNA5SP258
RN7SL651P
NEFL
SNORA67\|ENSG00000207027.1
FP15737
SLC25A37
TNFRSF10A
RN7SL303P
NUDT18
FGF17
snoU13\|ENSG00000238466.1
U3\|ENSG00000251944.1
SNORA62\|ENSG00000201157.1
RNA5SP256
MIR548V
MTMR7
ZDHHC2
FGF20
RN7SL474P
MIR383
RNA5SP255
LINC00681
FAM86B2
FAM66A
RNA5SP254
FAM66D
RNA5SP253
DEFB130\|ENSG00000233050.1
DEFB134
C8orf49
LINC00208
RN7SL293P
C8orf12
LINC00529
MIR598
SNORD112\|ENSG00000252565.1
SOX7
RNA5SP252
PRSS51
snoU13\|ENSG00000238496.1
snoU13\|ENSG00000239065.1
MIR597
U3\|ENSG00000252543.1
SNORA70\|ENSG00000207244.1
RN7SL178P
SGK223
ALG1L13P
FAM86B3P
LRLE1
FAM85B
FAM90A24P
FAM66E
DEFB105A
DEFB105B
DEFB103B
ZNF705G
FAM66B
XKR5
MIR4659A
AGPAT5
RN7SKP159
RN7SL318P
NAT1
NAT2
ADRA1A
ANGPT2
ASAH1
ATP6V1B2
BLK
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
CTSB
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
DPYSL2
DUSP4
EGR3
DMTN
EPHX2
EXTL3
PTK2B
FDFT1
FGL1
GATA4
GFRA2
GNRH1
GSR
GTF2E2
NRG1
LOXL2
LPL
MSR1
MSRA
NEFM
PDGFRL
PNOC
PPP2CB
PPP2R2A
PPP3CC
SFTPC
SLC7A2
SLC18A1
STC1
FZD3
TUSC3
TNKS
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
DOK2
MFHAS1
ENTPD4
PHYHIP
SORBS3
NPM2
DLC1
SPAG11B
DCTN6
PNMA2
ADAM28
RBPMS
LZTS1
XPO7
TRIM35
RHOBTB2
KIF13B
PSD3
LEPROTL1
SLC39A14
ADAMDEC1
CNOT7
PURG
SCARA3
TMEM66
KCTD9
PINX1
PIWIL2
ELP3
INTS10
CCDC25
INTS9
CSGALNACT1
HR
PBK
ZNF395
BIN3
TEX15
MTUS1
KIAA1456
KIAA1967
SH2D4A
PDLIM2
EBF2
FAM160B2
MTMR9
DUSP26
HMBOX1
MCPH1
PPP1R3B
RNF122
DOCK5
TTI2
REEP4
STMN4
SOX7
FAM167A
SLC35G5
MAK16
FUT10
FAM86B1
ERI1
LONRF1
CHMP7
RP1L1
CLDN23
VPS37A
SGCZ
UNC5D
DEFB104A
PEBP4
CDCA2
ESCO2
FBXO16
TDH
C8orf48
R3HCC1
PRSS55
C8orf74
LGI3
DEFB106A
DEFB107A
DEFB130\|ENSG00000232948.1
NEIL2
XKR6
MICU3
SCARA5
USP17L2
NUGGC
LINC00599
MIR320A
DEFB103A
DEFB107B
DEFB104B
DEFB106B
C8orf58
DEFB135
DEFB136
MBOAT4
SPAG11A
DEFA1B
ZNF705D
ZNF705B
DEFB4B
MIR548I3
MIR548H4
MIR3148
MIR4288
MIR4286
MIR3622B
SMIM18
MIR4660
MIR5692A2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q22.33.

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

Genes
FANCC
OMD
SYK
TAL2
XPA
NR4A3
FAM225A
FAM225B
ZNF883
INIP
C9orf147
RN7SL430P
RNA5SP295
RN7SL57P
MIR4668
UGCG
LRRC37A5P
RNA5SP294
RNY4P18
FRRS1L
MIR32
ACTL7B
RNA5SP293
RN7SL659P
RNA5SP292
RN7SKP77
RN7SKP191
RNA5SP291
LINC00587
TMEM246
SNORA31\|ENSG00000253041.1
LPPR1
RN7SKP87
MSANTD3
RN7SL75P
STX17
RN7SKP225
ALG2
RN7SL794P
RNA5SP290
CTSV
AAED1
LINC00092
RNA5SP289
DKFZP434H0512
LINC00476
snoU13\|ENSG00000238746.1
RNA5SP288
MIR27B
MIR23B
MIR2278
PCAT7
ZNF169
snoU13\|ENSG00000238792.1
MIRLET7DHG
CENPP
SNORA84
snoU13\|ENSG00000238996.1
LINC00475
LINC00484
MIR3153
SHC3
ABCA1
ALDOB
AUH
BAAT
CKS2
COL15A1
CYLC2
ECM2
LPAR1
S1PR3
FBP1
FKTN
FOXE1
GNG10
HSD17B3
IARS
MUSK
NCBP1
NFIL3
NINJ1
ROR2
OGN
PHF2
PPP3R2
PTCH1
PTPN3
RAD23B
TGFBR1
TMOD1
TXN
CORO2A
ZFP37
ZNF189
IKBKAP
CDC14B
TMEFF1
CTNNAL1
FBP2
KLF4
GABBR2
TRIM14
PTBP3
SEMA4D
ANP32B
SPTLC1
SMC2
ACTL7A
GADD45G
SEC61B
SLC35D2
AKAP2
ZNF510
HABP4
PTGR1
ERP44
FAM120A
BICD2
KIAA0368
TDRD7
SLC44A1
TMEM245
NIPSNAP3A
OR2K2
INVS
C9orf156
NANS
MRPL50
EPB41L4B
NUTM2F
DIRAS2
ASPN
TEX10
FAM206A
NOL8
TMEM38B
NIPSNAP3B
TBC1D2
HEMGN
BARX1
RNF20
SLC46A2
ZNF462
SUSD1
IPPK
WNK2
SECISBP2
GALNT12
SVEP1
ZNF484
FSD1L
HSDL2
C9orf89
HIATL2
HIATL1
C9orf3
FGD3
PALM2
GRIN3A
PTPDC1
ANKRD19P
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
FAM120AOS
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
ZNF367
ANKS6
SUSD3
TXNDC8
C9orf47
OR13C9
OR13D1
MURC
ERCC6L2
OR13C2
C9orf152
SNX30
MIRLET7A1
MIRLET7D
MIRLET7F1
NUTM2G
C9orf129
DNAJC25
MIR3074
MIR4291
MIR4290
MIR4289
CCDC180
MIR3927
MIR4670

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q25.

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

Genes
DDX6
PCSK7
SDHD
ATM
CBL
DDX10
FLI1
PAFAH1B2
POU2AF1
SDHD
ARHGEF12
snoU13\|ENSG00000238693.1
RNU6ATAC12P
RN7SL167P
LINC00167
KCNJ5
RN7SKP279
RN7SKP121
MIR3167
snoU13\|ENSG00000238855.1
RN7SL351P
KRT18P59
SLC37A2
RNA5SP352
TBRG1
OR10D3
U8\|ENSG00000200496.1
SNORD14C
SNORD14D
SNORD14E
snoU13\|ENSG00000239079.1
RNU4ATAC5P
RNU4ATAC10P
SC5D
TBCEL
OAF
THY1
MFRP
ACA64\|ENSG00000252119.1
HINFP
C2CD2L
MIR3656
RPS25
RN7SL529P
RN7SL688P
BCL9L
CXCR5
TTC36
RN7SL86P
CD3G
MPZL3
TMPRSS4
SCARNA11\|ENSG00000252992.1
RNY4P6
ZNF259
snoU13\|ENSG00000238625.1
LINC00900
snoU13\|ENSG00000239153.1
ACA59\|ENSG00000252870.1
snoU13\|ENSG00000238724.1
ATF4P4
snosnR66
C11orf34
RNA5SP351
HSPB2
ALG9
ALG9
RN7SKP273
SIK2
RNA5SP350
SNORD39\|ENSG00000264997.1
RNA5SP349
RNA5SP348
MMP12
ACAT1
ACRV1
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CASP1
CASP4
CASP5
CD3D
CD3E
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HTR3A
IL10RA
IL18
STT3A
KCNJ1
VWA5A
MCAM
KMT2A
MMP3
MMP13
NCAM1
NFRKB
NNMT
NPAT
NRGN
OPCML
PPP2R1B
PTS
PVRL1
RDX
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
UPK2
ZBTB16
ZNF202
CUL5
BARX2
USP2
HTR3B
ZW10
UBE4A
EI24
FEZ1
ARHGAP32
RBM7
MPZL2
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
IGSF9B
EXPH5
PHLDB1
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
REXO2
OR8B8
TIMM8B
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
NXPE4
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
IFT46
PRDM10
DSCAML1
GRAMD1B
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
TP53AIP1
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
DYNC2H1
NLRX1
MSANTD2
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
JAM3
BCO2
TMPRSS13
DCUN1D5
MSANTD4
KIRREL3
BUD13
TMEM25
RPUSD4
UBASH3B
DIXDC1
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
VPS26B
GLB1L3
TIRAP
CARD16
C1QTNF5
PANX3
APOA5
TMEM45B
C11orf93
PIH1D2
NXPE1
NXPE2
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
PATE1
C11orf65
ADAMTS15
C11orf45
HYLS1
TMEM218
OR8B12
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TMEM136
SPATA19
HEPACAM
ANKK1
RNF214
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
C11orf44
CCDC84
TMEM225
OR8D4
C11orf53
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
PATE2
PATE4
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
HEPN1
CLDN25
PATE3
MIR4301
CASP12
MIR4697
MIR4493
MIR4491
MIR4492
MIR4693

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p11.21.

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

Genes
MLLT10
RN7SL314P
NAMPTL
SNORA40\|ENSG00000237002.2
MIR4683
LINC00838
RN7SL398P
RN7SL847P
CCDC7
RN7SL825P
RNA5SP309
SVILP1
RN7SL63P
RN7SL241P
SNORD115\|ENSG00000212411.1
MIR604
PTCHD3P1
RNA5SP308
LINC00837
RNU4ATAC6P
RN7SKP39
U3\|ENSG00000222666.1
RN7SKP132
ARMC4P1
LINC00614
snoU13\|ENSG00000238414.1
SNORA57\|ENSG00000223027.1
LINC00264
RNA5SP307
RNA5SP306
RN7SKP220
RN7SKP241
RNA5SP305
MIR603
snoU13\|ENSG00000238515.1
SNORA40\|ENSG00000252049.1
RNA5SP304
RN7SKP37
RN7SKP219
MIR1915
CASC10
U3\|ENSG00000251749.1
RNA5SP303
U3\|ENSG00000200545.1
C10orf112
TMEM236\|ENSG00000184040.7
MRC1L1
snoR442\|ENSG00000251959.1
ST8SIA6
BMI1
CACNB2
MAP3K8
CREM
TRDMT1
GAD2
ITGB1
KIF5B
MRC1
PIP4K2A
SVIL
ZEB1
VIM
STAM
CUBN
FZD8
CUL2
NRP1
PTPLA
SPAG6
ABI1
NEBL
YME1L1
ANKRD26
MSRB2
RAB18
COMMD3
PDSS1
BAMBI
WAC
MYO3A
APBB1IP
ARMC4
MTPAP
KIAA1217
PARD3
PRTFDC1
ZNF248
GPR158
ARHGAP21
KIAA1462
DNAJC1
C10orf68
THNSL1
EPC1
LYZL1
PLXDC2
MASTL
ANKRD30A
ACBD5
ARHGAP12
LYZL2
MPP7
ENKUR
ARMC3
ZNF25
GJD4
CCNY
OTUD1
ZNF438
SLC39A12
NSUN6
ARL5B
PTF1A
C10orf67
MKX
C10orf126
EBLN1
PTCHD3
C10orf113
SKIDA1
C10orf115
LRRC37A6P
TMEM236\|ENSG00000148483.7
MIR938
MTRNR2L7
MIR3611
MIR4675

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.33.

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

Genes
ANHX
ZNF891
ZNF140
RNU4ATAC12P
RNA5SP379
LRCOL1
MUC8
SNORA49
RNA5SP378
RNA5SP377
RNA5SP376
RAN
snoU13\|ENSG00000238822.1
RN7SL534P
snoU13\|ENSG00000238895.1
MIR3612
TMEM132C
LINC00508
LINC00507
STX2
GOLGA3
MMP17
POLE
PXMP2
SFSWAP
ZNF10
ZNF26
ZNF84
ULK1
PIWIL1
ZNF268
FZD10
P2RX2
ANKLE2
RIMBP2
GALNT9
CHFR
EP400
FBRSL1
NOC4L
PUS1
TMEM132D
SLC15A4
GLT1D1
PGAM5
GPR133
DDX51
EP400NL
ZNF605
MIR4419B

Arm-level results

Table 3. Get Full Table Arm-level significance table - 30 significant results found. The significance cutoff is at Q value=0.25.

Arm	# Genes	Amp Frequency	Amp Z score	Amp Q value	Del Frequency	Del Z score	Del Q value
1p	1300	0.22	0.557	0.86	0.12	-4.14	1
1q	1195	0.33	4.81	4.6e-06	0.13	-3.93	1
2p	624	0.28	-0.436	1	0.19	-3.68	1
2q	967	0.16	-3.55	1	0.27	1.03	0.313
3p	644	0.38	4.01	0.000122	0.22	-2.19	1
3q	733	0.45	7.81	2.84e-14	0.13	-4.94	1
4p	289	0.13	-6.67	1	0.40	2.95	0.00439
4q	670	0.09	-7.14	1	0.36	3.48	0.000723
5p	183	0.39	2.13	0.0618	0.34	0.224	0.767
5q	905	0.15	-3.75	1	0.47	9.71	0
6p	710	0.22	-2.33	1	0.33	2.03	0.0514
6q	556	0.12	-5.75	1	0.44	6.41	4.15e-10
7p	389	0.43	4.8	4.6e-06	0.12	-6.6	1
7q	783	0.38	4.97	2.7e-06	0.13	-5.15	1
8p	338	0.30	-0.411	1	0.63	12.5	0
8q	551	0.52	9.08	0	0.25	-1.44	1
9p	301	0.27	-1.61	1	0.52	7.96	7.28e-15
9q	700	0.22	-2.04	1	0.49	8.84	0
10p	253	0.30	-1.02	1	0.31	-0.858	1
10q	738	0.12	-5.52	1	0.37	4.34	2.47e-05
11p	509	0.11	-6.31	1	0.48	7.58	1.21e-13
11q	975	0.16	-3.22	1	0.36	5.17	4.78e-07
12p	339	0.32	0.0515	1	0.20	-4.53	1
12q	904	0.25	-0.139	1	0.19	-2.53	1
13q	560	0.31	0.543	0.86	0.28	-0.593	1
14q	938	0.20	-2.04	1	0.34	4.06	7.82e-05
15q	810	0.13	-4.89	1	0.39	5.28	2.94e-07
16p	559	0.22	-2.63	1	0.35	2.36	0.0234
16q	455	0.25	-1.97	1	0.34	1.54	0.134
17p	415	0.22	-2.98	1	0.53	9	0
17q	972	0.36	4.7	5.88e-06	0.20	-1.92	1
18p	104	0.34	-0.269	1	0.37	0.992	0.314
18q	275	0.21	-4.09	1	0.44	4.4	1.98e-05
19p	681	0.24	-1.38	1	0.33	1.85	0.0731
19q	935	0.36	4.7	5.88e-06	0.24	-0.49	1
20p	234	0.53	8.22	1.52e-15	0.17	-5.05	1
20q	448	0.58	11.6	0	0.12	-5.53	1
21q	258	0.35	0.954	0.581	0.27	-2.09	1
22q	564	0.19	-3.45	1	0.44	6.3	7.49e-10
Xp	418	0.16	-5.66	1	0.24	-2.87	1
Xq	668	0.13	-6.12	1	0.24	-1.89	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/BLCA-TP/22213201/GDAC_MergeDataFiles_20403415/BLCA-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt
Markers File = /xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt
Reference Genome = /xchip/cga/reference/gistic2/hg19_GENCODE_v18_20140127.mat
CNV Files = /xchip/gistic/CNV/SNP6.merged.151117.hg19.CNV.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 408 Input Tumor Samples.

Tumor Sample Names
TCGA-2F-A9KO-01A-11D-A38F-01
TCGA-2F-A9KP-01A-11D-A38F-01
TCGA-2F-A9KQ-01A-11D-A38F-01
TCGA-2F-A9KR-01A-11D-A38F-01
TCGA-2F-A9KT-01A-11D-A38F-01
TCGA-2F-A9KW-01A-11D-A38F-01
TCGA-4Z-AA7M-01A-11D-A390-01
TCGA-4Z-AA7N-01A-11D-A390-01
TCGA-4Z-AA7O-01A-31D-A390-01
TCGA-4Z-AA7Q-01A-11D-A390-01

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:

Unique Name: A name assigned to identify the region.
Descriptor: The genomic descriptor of that region.
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.
Peak Limits: The boundaries of the region of maximal amplification or deletion.
Region Limits: The boundaries of the entire significant region of amplification or deletion.
Q values: The Q value of the peak region.
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.
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').
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:

Cytoband
Q value
Residual Q value
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)

[2] GISTIC version 1

[3] Mermel et al, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biology Vol. 12:4 (2011)

[4] GISTIC version 2

[5] Beroukhim et al., The landscape of somatic copy-number alteration across human cancers, Nature Vol. 463:7283 (2010)

[6] McCarroll, S. A. et al., Integrated detection and population-genetic analysis of SNPs and copy number variation, Nat Genet Vol. 40(10):1166-1174 (2008)

[7] The Sanger Institute: Cancer Gene Census

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