SNP6 Copy number analysis (GISTIC2) - Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)

SNP6 Copy number analysis (GISTIC2)

Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)

21 August 2015 | analyses__2015_08_21

Maintainer Information

Citation Information

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

Cite as Broad Institute TCGA Genome Data Analysis Center (2015): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1MC8Z59

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 295 tumor samples used in this analysis: 25 significant arm-level results, 28 significant focal amplifications, and 35 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 - 28 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
11q22.1	2.5504e-43	3.4578e-35	chr11:101626852-102266642	9
3q26.31	1.0426e-34	8.2574e-18	chr3:168026373-172485872	33
17q12	3.931e-13	4.0498e-12	chr17:37854508-37869191	1
3q28	4.165e-34	1.688e-11	chr3:189630382-189664399	0 [LEPREL1]
20q11.21	5.8527e-10	5.8527e-10	chr20:30204825-30356590	3
8q24.21	1.5065e-09	1.5065e-09	chr8:128754838-128772049	0 [MYC]
19q13.13	3.8863e-08	3.8863e-08	chr19:38356753-38956802	17
5p15.33	6.7894e-07	6.7894e-07	chr5:1-1322086	24
9p24.1	1.7114e-06	1.7114e-06	chr9:5302096-5565600	5
13q22.1	3.3022e-09	2.3855e-05	chr13:73929290-73956005	0 [LINC00393]
17q25.1	2.3855e-05	2.8809e-05	chr17:72966455-74083947	46
16p13.13	5.4137e-05	5.4137e-05	chr16:11883519-11927917	2
1q21.3	1.2368e-05	8.6123e-05	chr1:149939138-155333392	208
11q13.3	1.6896e-08	8.6123e-05	chr11:69512115-70378914	9
Xq28	8.6123e-05	8.6123e-05	chrX:152924807-155270560	76
6p21.33	0.0017776	0.0017776	chr6:30477277-30635592	9
15q26.1	0.006242	0.006242	chr15:74314461-102531392	285
7p11.2	0.0067959	0.0067959	chr7:54944574-55503308	2
2q33.1	0.014367	0.014367	chr2:173598160-202097179	160
13q34	0.0002278	0.021457	chr13:82939961-115169878	168
1p31.3	0.027432	0.027432	chr1:61416174-62488521	3
11p12	0.030188	0.031808	chr11:34553850-37667461	18
21q22.13	0.056412	0.056412	chr21:37471879-39171788	18
2p24.3	0.095396	0.095396	chr2:1-47640565	324
19p13.2	0.11379	0.14916	chr19:12898181-13077559	16
4q12	0.15662	0.15662	chr4:55996856-56580180	7
1q44	0.013243	0.19967	chr1:212684007-249250621	323
19p13.3	0.13245	0.20862	chr19:3333022-3533405	6

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q22.1.

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

Genes
BIRC3
snoU13\|ENSG00000239154.1
snoU13\|ENSG00000252679.1
BIRC2
TRPC6
YAP1
KIAA1377
C11orf70
ANGPTL5

Genes in Wide Peak

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

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

Genes
RN7SL141P
PP13439
snoU13\|ENSG00000238359.1
MIR569
RNY5P3
CLDN11
TERC
EGFEM1P
ECT2
MECOM
GHSR
PLD1
PRKCI
SKIL
SLC2A2
SEC62
TNFSF10
TNIK
GPR160
MYNN
EIF5A2
NCEH1
SLC7A14
FNDC3B
LRRC31
PHC3
ACTRT3
LRRC34
RPL22L1
LRRIQ4
SAMD7
TMEM212
MIR551B

Genes in Wide Peak

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

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

Genes
ERBB2

Genes in Wide Peak

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

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

Genes
BCL2L1
TPX2
COX4I2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.13.

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

Genes
SPRED3
snoU13\|ENSG00000238838.1
RN7SL663P
PSMD8
RYR1
DPF1
KCNK6
SPINT2
SIPA1L3
CATSPERG
C19orf33
WDR87
YIF1B
PPP1R14A
RASGRP4
FAM98C
GGN

Genes in Wide Peak

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

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

Genes
MIR4635
ZDHHC11B
CCDC127
LRRC14B
PLEKHG4B
SDHA
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
CEP72
AHRR
BRD9
ZDHHC11
CLPTM1L
NKD2
C5orf55
SLC6A19
SLC6A18
MIR4457
MIR4456

Genes in Wide Peak

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

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

Genes
CD274
RLN1
RLN2
PLGRKT
PDCD1LG2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q25.1.

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

Genes
MYO15B
RN7SL573P
ACOX1
CDK3
EVPL
GALK1
GRB2
H3F3B
ICT1
ITGB4
LLGL2
SUMO2
SRP68
GALR2
SLC16A5
RECQL5
KIAA0195
ATP5H
GGA3
EXOC7
KCTD2
WBP2
SAP30BP
NT5C
CDR2L
MRPS7
HN1
MIF4GD
CASKIN2
SLC25A19
MRPL38
ARMC7
NUP85
FBF1
UNK
TRIM47
TRIM65
UNC13D
HID1
TSEN54
ZACN
SMIM5
SMIM6
TEN1
MIR3678
MIR4738

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 16p13.13.

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

Genes
BCAR4
ZC3H7A

Genes in Wide Peak

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

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

Genes
ARNT
MUC1
TPM3
MIR555
GBAP1
EFNA3
MIR4258
SNORD59\|ENSG00000252682.1
SNORA58\|ENSG00000201129.1
C1orf189
RN7SL431P
MIR5698
U3\|ENSG00000252669.1
snoU13\|ENSG00000238511.1
RN7SL372P
RN7SL44P
S100A7L2
SPRR2B
SNORA31\|ENSG00000252920.1
LINC00302
NBPF18P
THEM4
LINGO4
CELF3
MIR554
SNORA44
RNY4P25
RN7SL444P
MLLT11
SNORA40\|ENSG00000253047.1
RN7SL600P
RN7SL473P
C1orf138
LINC00568
snoU13\|ENSG00000238526.1
RN7SL480P
OTUD7B
ADAR
CHRNB2
CKS1B\|ENSG00000173207.8
CLK2
CTSK
CTSS
ECM1
EFNA1
EFNA3
EFNA4
ENSA
FDPS
FLG
GBA
IL6R
ILF2
IVL
KCNN3
LOR
MCL1
SMCP
MTX1
NPR1
PI4KB
PKLR
PSMB4
PSMD4
RAB13
RFX5
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SPRR1A
SPRR1B
SPRR2A
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
VPS72
THBS3
TCHH
TUFT1
PIP5K1A
ANXA9
ADAM15
SELENBP1
PRPF3
SETDB1
UBAP2L
DENND4B
SCAMP3
HAX1
SEMA6C
PMVK
FAM189B
JTB
SLC27A3
TDRKH
VPS45
POGZ
RPRD2
SNAPIN
RUSC1
CA14
C1orf43
CHTOP
LCE2B
SLC39A1
TMOD4
CERS2
CRNN
ZBTB7B
APH1A
PLEKHO1
OAZ3
DPM3
MRPS21
ADAMTSL4
CRCT1
C1orf56
GOLPH3L
UBE2Q1
FAM63A
ASH1L
LENEP
SLC50A1
CDC42SE1
PGLYRP4
ATP8B2
PBXIP1
S100A14
GATAD2B
CGN
ZNF687
HCN3
PRUNE
MRPL9
INTS3
SCNM1
TNFAIP8L2
C1orf54
TRIM46
TARS2
FLAD1
SNX27
ANP32E
HORMAD1
LCE3D
AQP10
PYGO2
NUP210L
PGLYRP3
GABPB2
TCHHL1
RPTN
TDRD10
SHE
DCST2
S100A16
CREB3L4
C1orf51
LELP1
DCST1
BNIPL
SPRR4
LCE4A
KRTCAP2
CRTC2
LCE5A
RIIAD1
THEM5
S100A7A
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
LYSMD1
HRNR
FLG2
KPRP
LCE6A
PRR9
MIR92B
MIR190B
C1orf68
C2CD4D
MIR4257

Genes in Wide Peak

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

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

Genes
MIR548K
FGF3
CTTN
FGF4
PPFIA1
FADD
FGF19
SHANK2
ANO1

Genes in Wide Peak

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

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

Genes
MTCP1
WASH6P\|ENSG00000182484.10
WASIR1\|ENSG00000185203.7
F8A3
F8A2
FUNDC2
SNORA56
SNORA36A
RN7SL742P
RN7SL697P
LAGE3
SNORA70\|ENSG00000207165.1
TEX28P1
OPN1MW
TEX28P2
NAA10
LCA10
SNORD36\|ENSG00000251846.1
RN7SL687P
ABCD1
ARHGAP4
ATP6AP1
AVPR2
CLIC2
CTAG1B
TEX28
DKC1
DNASE1L1
EMD
F8
FLNA
G6PD
GDI1
HCFC1
IDH3G
IL9R\|ENSG00000124334.12
IRAK1
L1CAM
MECP2
MPP1
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SSR4
VAMP7\|ENSG00000124333.10
TAZ
VBP1
F8A1
UBL4A
TMEM187
SLC10A3
TKTL1
IKBKG
FAM50A
BCAP31
SPRY3\|ENSG00000168939.6
SRPK3
CTAG2
TMLHE
PLXNA3
PDZD4
FAM3A
BRCC3
H2AFB3
RAB39B
GAB3
PNCK
CTAG1A
H2AFB2
H2AFB1
OPN1MW2
SMIM9
CMC4
MIR718

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.33.

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

Genes
MIR877
PRR3
ABCF1
GNL1
PPP1R10
DHX16
MRPS18B
ATAT1
C6orf136

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 15q26.1.

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

Genes
BLM
IDH2
NTRK3
PML
CRTC3
DDX11L9
WASH3P
FAM138E
OR4F13P
RN7SL209P
DNM1P47
snoU13\|ENSG00000238502.1
LINS
RNA5SP402
RN7SL484P
DKFZP779J2370
MIR4714
RNA5SP401
RN7SL677P
RN7SKP181
RN7SKP254
MIR1469
LINC00924
MIR3175
RN7SL599P
LINC00930
snoU109\|ENSG00000239197.1
snoU13\|ENSG00000238981.1
RN7SL363P
SNORD18\|ENSG00000200677.1
ZNF774
GABARAPL3
RN7SL736P
CIB1
RN7SL346P
RN7SL755P
C15orf38
MIR5009
MIR5094
MESP1
LINC00928
LINC00925
ISG20
SNORD74\|ENSG00000200206.1
RNA5SP400
RN7SL428P
CSPG4P12
SNORA25\|ENSG00000200991.1
LINC00933
GOLGA6L5
CSPG4P5
RN7SL417P
GOLGA6L4
RN7SL331P
EFTUD1P1
HDGFRP3
SCARNA15\|ENSG00000252690.2
GOLGA6L10\|ENSG00000254374.2
RN7SL410P
GOLGA6L9\|ENSG00000196648.6
UBE2Q2P3
RN7SL256P
RN7SL61P
CSPG4P8
UBE2Q2P2
TMC3
STARD5
LINC00927
SNORD112\|ENSG00000251881.1
C15orf37
MTHFS
ANKRD34C
CTSH
ACSBG1
IDH3A
SNORA63\|ENSG00000199633.1
SH2D7
MIR1827
RN7SL214P
RN7SL278P
RN7SKP217
NRG4
RN7SL510P
SNORD112\|ENSG00000252372.1
RN7SL319P
DNM1P35
SNX33
ANP32BP1
DNM1P34
RN7SL327P
GOLGA6D
RN7SL489P
GOLGA6C
SCARNA20\|ENSG00000252722.1
RPP25
COX5A
SCAMP2
SNORD77\|ENSG00000212279.2
RN7SL429P
ACAN
ALDH1A3
ANPEP
BCL2A1
BNC1
CHD2
CHRNA3
CHRNA5
CHRNB4
CLK3
CRABP1
CSK
CSPG4
CYP1A1
CYP1A2
CYP11A1
ETFA
FAH
FES
IGF1R
IL16
IREB2
ISLR
MAN2A2
MAN2C1
MEF2A
MFGE8
MPI
NMB
FURIN
PCSK6
PDE8A
PLIN1
POLG
PSMA4
PTPN9
RASGRF1
RCN2
RLBP1
RPS17
SH3GL3
SNRPA1
NR2F2
AP3B2
ST8SIA2
SEMA7A
PEX11A
IQGAP1
PSTPIP1
PRC1
SLC28A1
HOMER2
ZNF592
SV2B
ARNT2
SNUPN
TSPAN3
AP3S2
HMG20A
SEMA4B
CIB2
ARID3B
MORF4L1
ABHD2
ADAMTS7
AKAP13
CHSY1
TBC1D2B
MESDC2
KIAA1024
SYNM
TMED3
SEC11A
SIN3A
ULK3
FBXO22
VPS33B
MRPL46
OR4F4
SLCO3A1
SCAPER
NGRN
RHCG
BTBD1
TM6SF1
ZFAND6
SCAND2P
COMMD4
ZSCAN2
DET1
FANCI
IMP3
DNAJA4
MCTP2
VIMP
UNC45A
C15orf39
RGMA
WDR93
FAM219B
ADAMTSL3
KIAA1199
ALPK3
ISLR2
ABHD17C
MESDC1
PPCDC
STRA6
KLHL25
CPEB1
AEN
ISL2
TTC23
MRPS11
EFTUD1
NEIL1
LRRK1
LMAN1L
PEAK1
CCDC33
EDC3
TM2D3
WDR61
FAM103A1
MEX3B
LINGO1
WDR73
UBL7
TICRR
RCCD1
ARRDC4
LINC00923
UBE2Q2
C15orf40
TARSL2
LRRC28
C15orf27
AGBL1
HYKK
WHAMM
FSD2
ASB7
LYSMD4
PGPEP1L
C15orf32
HAPLN3
MESP2
SPATA8
LINC00052
C15orf26
ODF3L1
ADAMTS17
SCAMP5
DNM1P46
CERS3
C15ORF37
FAM154B
FAM169B
GOLGA6A
KIF7
ZNF710
HDDC3
UBE2Q2P1
SPATA41
GDPGP1
OR4F6
OR4F15
ST20
FAM174B
MIR184
GOLGA6L9\|ENSG00000197978.8
TTLL13
CPLX3
GOLGA6L10\|ENSG00000205281.6
MIR549
MIR631
MIR1276
MIR1179
MIR3174
MIR4313
MIR3713
RPS17L
MIR4514
MIR4513
MIR4515
MIR548AP

Genes in Wide Peak

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

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

Genes
EGFR
LANCL2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2q33.1.

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

Genes
HOXD11
CHN1
HOXD13
NFE2L2
PMS1
RN7SL694P
ORC2
RNA5SP115
AOX2P
RN7SL717P
PLCL1
RFTN2
MOB4
SNORA4\|ENSG00000202434.1
C2orf66
SCARNA16\|ENSG00000252923.1
RN7SL820P
snoU13\|ENSG00000239161.1
SNORD59\|ENSG00000252517.1
PCGEM1
NABP1
RN7SKP179
TMEM194B
MIR3129
MIR1245A
DIRC1
GULP1
RNA5SP114
RN7SKP42
U8\|ENSG00000212581.1
snoU13\|ENSG00000238306.1
SNORA77\|ENSG00000221498.1
DNAJC10
RN7SL267P
RNA5SP113
RNU6ATAC19P
SNORA43\|ENSG00000202216.1
snoU13\|ENSG00000238339.1
ACA59\|ENSG00000252000.1
PLEKHA3
TTC30A
TTC30B
snoU13\|ENSG00000238295.1
MIR3128
RNA5SP112
RNU6ATAC14P
HOXD9
EVX2
KIAA1715
ATP5G3
SP9
RN7SL65P
AOX1
CASP10
CHRNA1
CLK1
COL3A1
COL5A2
ATF2
FRZB
MSTN
GLS
HOXD1
HOXD3
HOXD4
HOXD8
HOXD10
HOXD12
HSPD1
HSPE1
INPP1
ITGA4
ITGAV
MYO1B
NAB1
NDUFB3
NEUROD1
PDE1A
SP3
SSFA2
STAT1
STAT4
TFPI
TTN
WIPF1
SDPR
AGPS
PRKRA
CFLAR
STK17B
GTF3C3
CIR1
BZW1
CALCRL
UBE2E3
MTX2
NCKAP1
RAPGEF4
SATB2
SF3B1
TMEFF2
MOB4
SPATS2L
HIBCH
OLA1
SLC40A1
PDE11A
FKBP7
MLTK
PPIL3
ASNSD1
MFSD6
ZC3H15
DNAH7
SLC39A10
HECW2
CWC22
NIF3L1
OSGEPL1
BOLL
C2orf47
SCRN3
PGAP1
COQ10B
CDCA7
WDR75
C2orf88
SESTD1
ANKRD44
ZNF804A
MARS2
ORMDL1
OSBPL6
NUP35
TYW5
RBM45
KCTD18
DUSP19
ANKAR
ZSWIM2
ZNF385B
PPP1R1C
SGOL2
GPR155
FAM171B
C2orf69
HNRNPA3
CCDC150
CCDC141
FAM126B
FTCDNL1
CERKL
FSIP2
MIR10B
DFNB59
MIR561
MIR933
MIR1258
MIR4437
MIR548AE1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 13q34.

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

Genes
ERCC5
MIR548AR
LINC00565
LINC00452
LINC00453
LINC00454
GRK1
DCUN1D2
LINC00403
LINC00404
SNORD44
LINC00354
LINC00346
LINC00567
snoU13\|ENSG00000238629.1
RN7SL783P
RN7SKP10
LINC00676
RNA5SP39
MIR1267
SNORD31
LINC00443
LINC00551
ARGLU1
LINC00460
RNA5SP38
SNORA25\|ENSG00000252550.1
LINC00344
LINC00343
METTL21EP
RNY5P8
LINC00283
CCDC168
snoU13\|ENSG00000238869.1
LINC00555
MIR4705
RNY1P2
MIR2681
FGF14
LINC00411
GGACT
LINC00554
snoU13\|ENSG00000238305.1
SNORA25\|ENSG00000201245.1
MIR4306
RNY3P6
LINC00449
MIR623
RN7SKP9
RN7SL60P
RN7SKP8
snoU13\|ENSG00000238407.1
RAP2A
RNA5SP37
snoU13\|ENSG00000238522.1
SNORD112\|ENSG00000252154.1
RN7SKP7
LINC00359
RN7SL164P
HS6ST3
snR65\|ENSG00000251901.1
RNY4P27
RNY3P8
snoU13\|ENSG00000238463.1
LINC00557
LINC00391
RN7SL585P
RNA5SP36
RNA5SP35
SNORD22
MIR548AS
RNU4ATAC3P
LINC00379
LINC00410
RNA5SP34
LINC00559
SNORD38\|ENSG00000200733.1
LINC00353
LINC00440
LINC00560
LINC00433
MIR4500HG
LINC00351
LINC00333
ATP4B
COL4A1
COL4A2
DCT
GPR183
EFNB2
F7
F10
GPC5
GAS6
GPR18
ING1
IPO5
LAMP1
LIG4
PCCA
DNAJC3
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
ZIC2
STK24
CUL4A
IRS2
PROZ
ARHGEF7
CDC16
CLDN10
ITGBL1
TM9SF2
GPC6
MBNL2
FARP1
ABCC4
TUBGCP3
TNFSF13B
SOX21
RASA3
DZIP1
MYO16
ATP11A
MCF2L
DOCK9
TGDS
SLITRK5
OXGR1
BIVM
TMCO3
ANKRD10
RAB20
CARKD
UGGT2
PCID2
UPF3A
KDELC1
CARS2
GRTP1
SLITRK6
TMTC4
ABHD13
ZIC5
TEX30
ADPRHL1
SLITRK1
TEX29
SPACA7
RNF113B
GPR180
CLYBL
METTL21C
NALCN
DAOA
CHAMP1
UBAC2
TMEM255B
C13orf35
MIR17HG
MIR622
FAM155A
MIR3170
MIR4500
MIR4502

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p31.3.

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

Genes
NFIA
INADL
TM2D1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p12.

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

Genes
TRAF6
COMMD9
MIR3973
TRIM44
MIR1343
EHF
CD44
RAG1
RAG2
SLC1A2
PDHX
FJX1
PAMR1
APIP
PRR5L
C11orf74
LDLRAD3
LINC00610

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 21q22.13.

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

Genes
KCNJ6
RN7SL678P
RNA5SP491
CHAF1B
snoU13\|ENSG00000238851.1
RN7SL73P
CBR3
DYRK1A
HLCS
SIM2
TTC3
DOPEY2
DSCR3
MORC3
CLDN14
PIGP
RIPPLY3
DSCR9

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p24.3.

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

Genes
ALK
DNMT3A
MSH2
MYCN
NCOA1
EML4
MIR559
RN7SKP119
BCYRN1
RHOQ
RN7SL817P
RN7SL414P
SLC3A1
snoU13\|ENSG00000239052.1
RN7SKP66
SNORD75\|ENSG00000221300.1
snoZ247
HNRNPA1P57
SNORA67\|ENSG00000252473.1
RN7SL96P
GEMIN6
LINC00211
RN7SL602P
RNA5SP92
RNA5SP91
SNORD112\|ENSG00000252502.1
LINC00486
MIR4765
MIR558
YIPF4
DPY30
SRD5A2
EHD3
RNA5SP90
SNORA64\|ENSG00000207187.1
RN7SL516P
SNORD53
SNORD92
RNA5SP89
FOSL2
MIR4263
RBKS
SNORA36\|ENSG00000206731.1
UCN
TCF23
KCNK3
RN7SL856P
EFR3B
SNORD14
PTRHD1
RNA5SP88
SCARNA21\|ENSG00000251805.1
PFN4
RN7SL610P
UBXN2A
RN7SKP27
RNA5SP87
RN7SL117P
TDRD15
GDF7
RNA5SP86
RN7SL140P
LINC00954
SNORA40\|ENSG00000212455.1
RN7SKP168
SNORA40\|ENSG00000251704.1
RN7SL104P
MYCNOS
snoU13\|ENSG00000238371.1
LINC00276
MIR3125
SNORD18\|ENSG00000238503.1
MIR548S
RN7SL674P
RNA5SP85
RNA5SP84
LINC00570
RN7SL832P
SNORA80B
SNORA51\|ENSG00000206898.1
RN7SL66P
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
ADCY3
APOB
RHOB
ZFP36L2
CAD
CALM2
CENPA
CYP1B1
DDX1
DTNB
E2F6
EPAS1
FKBP1B
GCKR
GTF3C2
HADHA
HADHB
HPCAL1
ID2
KCNF1
KCNS3
KHK
KIF3C
LTBP1
EPCAM
MATN3
MPV17
ODC1
VIT
PIGF
POMC
PPM1B
PPM1G
PPP1CB
PRKCE
EIF2AK2
RPS7
RRM2
SDC1
SRSF7
SIX3
SLC8A1
SOS1
SOX11
SPAST
STRN
ADAM17
TPO
TSSC1
VSNL1
XDH
SLC30A3
PXDN
KLF11
MAP4K3
ASAP2
SLC5A6
EIF2B4
TAF1B
COX7A2L
ITGB1BP1
OTOF
CRIPT
ROCK2
TP53I3
MRPL33
BRE
PREPL
FEZ2
SOCS5
GREB1
LAPTM4A
RNF144A
SNX17
SUPT7L
PREB
LRPPRC
PDIA6
CEBPZ
CDC42EP3
CGREF1
SIX2
RAB10
YWHAQ
EMILIN1
GPN1
MAPRE3
SLC4A1AP
MYT1L
WDR43
LPIN1
PUM2
HAAO
NTSR2
PRKD3
RASGRP3
QPCT
FAM98A
IFT172
SH3YL1
TRIB2
GRHL1
NRBP1
ITSN2
MEMO1
TRAPPC12
CRIM1
DNAJC27
ATRAID
NBAS
DYNC2LI1
SF3B14
YPEL5
CPSF3
SNTG2
ATAD2B
HEATR5B
TMEM214
SLC35F6
TRMT61B
SRBD1
ASXL2
ADI1
NDUFAF7
TTC27
SLC30A6
ALLC
DPYSL5
TRIM54
TTC7A
BIRC6
KIDINS220
MTA3
WDR35
RDH14
NLRC4
AGBL5
C2orf43
THADA
ATL2
ABCG5
ABCG8
HS1BP3
FNDC4
COLEC11
CENPO
GALNT14
CCDC121
SMC6
CLIP4
CAMKMT
NOL10
C2orf44
THUMPD2
FAM49A
LBH
C2orf16
ZNF512
ABHD1
EPT1
MCFD2
ATP6V1E2
DHX57
PKDCC
RSAD2
CAPN13
DRC1
HNRNPLL
NT5C1B
KLHL29
CMPK2
CIB4
PLEKHH2
OSR1
TTC32
ZNF513
GALM
TMEM178A
C2orf50
PQLC3
GAREML
PLB1
MYADML
FAM84A
RMDN2
GPR113
OXER1
FAM179A
KCNG3
CYS1
KRTCAP3
SPDYA
ATP6V1C2
RNASEH1
LCLAT1
GPATCH11
FAM150B
C2orf61
DNAJC5G
C2orf70
C2orf53
LINC00299
MSGN1
CDKL4
GEN1
C2orf48
FAM228B
MFSD2B
C2orf71
TMEM247
SULT6B1
LINC00487
C2orf91
CAPN14
FAM228A
RAD51AP2
MORN2
OST4
ARHGEF33
MIR1301
MIR4261
MIR4262
MIR3681
MIR4757
MIR4429
MIR548AD

Genes in Wide Peak

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

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

Genes
SYCE2
CALR
DNASE2
FARSA
GCDH
JUNB
RAD23A
PRDX2
RNASEH2A
KLF1
MAST1
HOOK2
RTBDN
GADD45GIP1
DAND5
MIR5695

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q12.

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

Genes
RN7SKP30
RN7SL822P
CLOCK
NMU
TMEM165
SRD5A3
PDCL2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q44.

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

Genes
FH
PGBD2
LYPD8
OR2T7
OR2AJ1
TRIM58
OR1C1
OR14K1
OR14A2
OR2W5
RNA5SP82
MIR3916
ZNF670
SNORA25\|ENSG00000252011.1
SNORD112\|ENSG00000252495.1
RN7SKP55
RN7SL148P
MIR4677
RN7SKP12
RNA5SP81
CHRM3
MTRNR2L11
ZP4
SNORA25\|ENSG00000252290.1
MIR4428
RN7SKP195
snoU13\|ENSG00000252638.1
MIR4753
SNORA14B
RN7SL668P
RNY4P16
LINC00184
U8\|ENSG00000212144.1
MIR4671
MIR4427
NTPCR
RN7SL299P
LINC00582
TRAX
RNA5SP80
MIR1182
snoU13\|ENSG00000238985.1
RN7SL837P
RNA5SP79
RN7SL467P
RNA5SP78
RN7SKP276
TMEM78
SNORA51\|ENSG00000206878.1
RNA5SP18
RNA5S17
RNA5S16
RNA5S15
RNA5S14
RNA5S13
RNA5S12
RNA5S11
RNA5S10
RNA5S9
RNA5S8
RNA5S7
RNA5S6
RNA5S5
RNA5S4
RNA5S3
RNA5S2
RNA5S1
RNA5SP19
BTNL10
RNF187
MIR3620
MIR5008
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
ACTA1
ACTN2
PARP1
ADSS
AGT
ARF1
ATF3
CAPN2
CENPF
CHML
LYST
EPHX1
EPRS
ESRRG
GALNT2
GNG4
GUK1
H3F3A
HNRNPU
ITPKB
KCNK1
KCNK2
LBR
LGALS8
MARK1
MTR
NID1
NVL
PROX1
PSEN2
PTPN14
RAB4A
RGS7
RYR2
SRP9
TARBP1
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TP53BP2
TSNAX
USH2A
ZNF124
HIST3H3
GNPAT
CDC42BPA
DEGS1
KMO
TAF1A
EXO1
GGPS1
TMEM63A
TOMM20
URB2
CEP170
AKT3
BPNT1
ZBTB18
LEFTY1
SPHAR
CAPN9
SDCCAG8
DUSP10
COG2
RBM34
FBXO28
ABCB10
OPN3
RAB3GAP2
AHCTF1
NSL1
OR2M4
OR2L2
OR2T1
RPS6KC1
TAF5L
DISC1
FLVCR1
CNIH4
PYCR2
RRP15
DESI2
SCCPDH
TRIM17
KCTD3
ARID4B
EGLN1
MAP10
MARC2
SUSD4
KIF26B
GPATCH2
HEATR1
BATF3
ZNF692
IARS2
ENAH
NUP133
ERO1LB
FMN2
SMYD2
ADCK3
ZNF695
GJC2
SIPA1L2
RHOU
TFB2M
GREM2
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
SH3BP5L
OR2L5
OR2G3
OR2G2
OR2C3
TRIM11
MIXL1
SPRTN
OBSCN
EFCAB2
MLK4
ZNF496
C1orf198
DISP1
WNT3A
ANGEL2
HIST3H2A
NLRP3
COX20
SNAP47
CCSAP
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
DNAH14
OR2B11
WDR64
C1orf131
EDARADD
MRPL55
HIST3H2BB
TATDN3
BROX
SLC35F3
B3GALNT2
GCSAML
CNIH3
EXOC8
C1orf227
FAM71A
SDE2
CNST
C1orf65
PLD5
C1orf100
IBA57
OR2T6
C1orf101
OR2L13
OR14A16
LIN9
PRSS38
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
MIA3
C1orf95
FAM89A
COA6
C1orf229
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
FAM177B
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MIR215
TRIM67
MAP1LC3C
OR13G1
C1orf145
C1orf148
MT1HL1
MIR1537
MIR3123
MIR3124
MIR3916
MIR4666A

Genes in Wide Peak

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

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

Genes
SNORD38\|ENSG00000252408.1
FZR1
RN7SL866P
NFIC
DOHH
C19orf77

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 - 35 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
2q37.1	2.9364e-41	3.6105e-32	chr2:230574908-243199373	150
19p13.3	2.1153e-25	2.1153e-25	chr19:1103802-1272039	6
2q22.1	3.1957e-32	2.9138e-24	chr2:140708948-143637838	2
11q25	2.9836e-31	5.7933e-20	chr11:129148160-132285294	15
13q14.2	4.6962e-19	1.6404e-15	chr13:40171063-54691766	140
4q35.2	1.8583e-13	1.6972e-12	chr4:187179487-191154276	18
10q23.31	7.4464e-10	7.4464e-10	chr10:89617158-90034038	3
3p14.2	2.1054e-09	2.1054e-09	chr3:59034763-61547330	3
20p12.1	3.7932e-08	3.7932e-08	chr20:14301156-16252980	2
11q23.3	3.6752e-33	2.6056e-06	chr11:105849158-131242853	276
6q26	0.00011216	0.00010719	chr6:155575868-171115067	94
15q21.1	0.00046821	0.00046821	chr15:37383162-57887323	219
17q25.3	0.00067668	0.00069907	chr17:79510900-81195210	56
1p36.23	0.00027743	0.00070343	chr1:1-28840301	481
5q12.1	0.00042129	0.00075554	chr5:58151172-59818245	3
14q32.31	0.00084671	0.00084671	chr14:89164454-107349540	270
16q23.1	0.00064682	0.0009109	chr16:78098006-79299841	3
22q13.32	0.0012674	0.0013153	chr22:48026910-51304566	42
7q34	0.0015497	0.0015565	chr7:120935777-159138663	340
18q21.2	0.0017822	0.0017543	chr18:48472083-48650073	3
4q22.1	0.00068089	0.0078516	chr4:91271445-93240505	1
Xq21.33	0.0085816	0.0083307	chrX:96134519-99356556	3
1p13.2	0.012262	0.02114	chr1:90490107-149898950	320
13q12.11	2.3424e-09	0.02298	chr13:1-26521598	73
16q11.2	0.016575	0.025088	chr16:31804435-61681921	155
8p23.1	0.0011222	0.025088	chr8:11272209-11352540	1
19q13.33	0.025088	0.025088	chr19:45821186-59128983	551
Xp11.3	0.025141	0.025088	chrX:44702452-45008304	2
6p24.2	0.02614	0.02614	chr6:1-26184040	171
17p12	0.02912	0.028732	chr17:11919496-12456081	2
11p15.1	0.030172	0.030495	chr11:1-28133205	371
4q21.3	0.0015773	0.033309	chr4:87503395-87746054	1
8p23.3	0.0024768	0.095141	chr8:1-4251018	14
21q11.2	0.19618	0.19414	chr21:1-34398715	96
5q35.2	0.097803	0.22125	chr5:175053854-175224904	2

Genes in Wide Peak

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

Table S26. 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
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BOK
CHRNG
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
HTR2B
SP110
INPP5D
KCNJ13
NDUFA10
SEPT2
NEU2
PDCD1
PDE6D
PPP1R7
PSMD1
PTMA
SAG
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
ATG16L1
USP40
HJURP
HES6
ACKR3
GAL3ST2
RAB17
COPS7B
TRPM8
MLPH
IQCA1
C2orf54
ARMC9
EFHD1
ILKAP
ITM2C
ING5
B3GNT7
SP140L
AGAP1
TWIST2
DIS3L2
NEU4
SPATA3
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
SLC16A14
LINC00471
C2orf57
TIGD1
C2orf72
DUSP28
MROH2A
ESPNL
AQP12A
KLHL30
C2orf82
OR6B2
ASB18
PRR21
PRSS56
AQP12B
D2HGDH
MIR1471
MIR4269
MIR4786
MIR5001

Genes in Wide Peak

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

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

Genes
STK11
ATP5D
GPX4
SBNO2
MIDN
C19orf26

Genes in Wide Peak

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

Table S28. 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 11q25.

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

Genes
RNU6ATAC12P
RN7SL167P
LINC00167
APLP2
NFRKB
ST14
BARX2
ADAMTS8
ZBTB44
NTM
PRDM10
TMEM45B
ADAMTS15
C11orf44
SNX19

Genes in Wide Peak

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

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

Genes
LCP1
RB1
LINC00558
RN7SL618P
SUGT1
LINC00345
RNY4P24
RN7SL413P
RNY1P6
RN7SL320P
RPS4XP16
LINC00371
RNA5SP29
RNA5SP28
DLEU7
RNY4P9
RNY4P30
RNY3P2
LINC00462
LINC00441
LINC00562
LINC00444
RN7SL700P
LINC00563
RN7SKP5
snoU13\|ENSG00000238483.1
RN7SL288P
RNA5SP27
SNORA31\|ENSG00000199477.1
SNORA31\|ENSG00000253051.1
7SK\|ENSG00000271818.1
RN7SKP3
RN7SL49P
LINC00330
snoU13\|ENSG00000238932.1
TSC22D1
LINC00284
LINC00400
RN7SL515P
MIR5006
KBTBD7
snoU13\|ENSG00000238651.1
RN7SL597P
SUGT1P3
TPTE2P5
SLC25A15
LINC00598
RN7SKP2
RNY3P9
LINC00332
SNORD116\|ENSG00000212553.1
RNY4P14
ATP7B
RCBTB2
CPB2
ELF1
ESD
FOXO1
MLNR
GTF2F2
GUCY1B2
HTR2A
KPNA3
NEK3
PCDH8
TPT1
TNFSF11
SUCLA2
ITM2B
MTRF1
UTP14C
LPAR6
TRIM13
MRPS31
DLEU1
OLFM4
LECT1
WBP4
AKAP11
FNDC3A
VWA8
ZC3H13
LRCH1
INTS6
CKAP2
NUFIP1
RGCC
MED4
DNAJC15
VPS36
PHF11
ENOX1
RCBTB1
NUDT15
KIAA1704
THSD1
CYSLTR2
SPRYD7
COG6
SMIM2
NAA16
RNASEH2B
DHRS12
KIAA0226L
CDADC1
CAB39L
CCDC70
COG3
SETDB2
EBPL
KBTBD6
EPSTI1
ARL11
WDFY2
FAM216B
LACC1
HNRNPA1L2
DGKH
CCDC122
FAM194B
SPERT
FAM124A
LRRC63
SLC25A30
SIAH3
KCNRG
NEK5
KCTD4
SERP2
DLEU2
ALG11
SERPINE3
MIR621
MIR759
MIR320D1
MIR3168
MIR4305
MIR3613
MIR4703
MIR5693

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.2.

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

Genes
DUX4
RNA5SP175
RNA5SP174
HSP90AA4P
F11
FAT1
FRG1
MTNR1A
ZFP42
TRIML2
TRIML1
DUX4L4
FRG2
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2

Genes in Wide Peak

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

Table S32. 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 3p14.2.

Table S33. 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 20p12.1.

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

Genes
RNA5SP475
FLRT3

Genes in Wide Peak

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

Table S35. 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
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
ACAT1
ACRV1
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CD3D
CD3E
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
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
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
AASDHPPT
PKNOX2
TP53AIP1
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
NLRX1
MSANTD2
CLMP
PDZD3
C11orf63
CCDC15
TMPRSS5
PUS3
MFRP
BCO2
TMPRSS13
MSANTD4
KIRREL3
BUD13
TMEM25
RPUSD4
UBASH3B
DIXDC1
ZC3H12C
ESAM
ALKBH8
FDXACB1
C11orf52
TIRAP
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
BLID
HEPN1
CLDN25
PATE3
MIR4301
MIR4493
MIR4491
MIR4492

Genes in Wide Peak

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

Table S36. 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
ACAT2
CCR6
IGF2R
KIF25
LPA
MAS1
MAP3K4
PARK2
PDCD2
PLG
PSMB1
RPS6KA2
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCP1
TCTE3
DYNLT1
THBS2
EZR
RNASET2
SYNJ2
QKI
WTAP
PDE10A
C6orf123
DLL1
MRPL18
CLDN20
NOX3
SNX9
MPC1
UNC93A
PHF10
C6orf70
AGPAT4
TULP4
ARID1B
TMEM181
SMOC2
ZDHHC14
FRMD1
LINC00574
LPAL2
RSPH3
FAM120B
FNDC1
SERAC1
SYTL3
TAGAP
PACRG
PNLDC1
DACT2
C6orf118
OSTCP1
WDR27
PRR18
C6orf120
TCP10L2
LINC00242
GTF2H5
TMEM242
MIR1202
MIR3918
MIR3939
MIR4466

Genes in Wide Peak

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

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

Genes
BUB1B
TCF12
LINC00926
snoU13\|ENSG00000239035.1
RN7SL568P
snoU13\|ENSG00000238513.1
PYGO1
MIR628
RSL24D1
ONECUT1
MIR1266
U6\|ENSG00000272337.1
RN7SL354P
RNA5SP395
U6\|ENSG00000271819.1
RN7SL494P
RNA5SP394
FGF7
RN7SL307P
RN7SL577P
RN7SKP139
FKSG62
RN7SKP101
SNORD11\|ENSG00000238819.1
SNORA41\|ENSG00000207516.1
HMGN2P46
snoU13\|ENSG00000238583.1
SLC30A4
SNORA11\|ENSG00000261709.2
SORD
B2M
RN7SL347P
HYPK
CATSPER2P1
snoU13\|ENSG00000238494.1
snoU13\|ENSG00000238535.1
RN7SL487P
CCNDBP1
snoU13\|ENSG00000239025.1
MIR627
MIR4310
RNA5SP393
MIR626
RN7SL497P
RN7SL376P
snoU13\|ENSG00000238559.1
LINC00594
RNA5SP392
LINC00984
snoU13\|ENSG00000238564.1
THBS1
FAM98B
CAPN3
CKMT1B
CYP19A1
DUT
EPB42
FBN1
GABPB1
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
ITPKA
IVD
LTK
MAP1A
MFAP1
MYO5A
NEDD4
PLCB2
MAPK6
RAB27A
RAD51
SLC12A1
SPINT1
SRP14
TP53BP1
TYRO3
EIF3J
SNAP23
USP8
SLC28A2
CCPG1
COPS2
TGM5
PIGB
PPIP5K1
SECISBP2L
LCMT2
BCL2L10
RASGRP1
GNB5
ARPP19
SLC27A2
GPR176
CHP1
OIP5
BAHD1
CEP152
MAPKBP1
RTF1
MGA
DMXL2
VPS39
AP4E1
EID1
SERF2
TMEM87A
RPAP1
BLOC1S6
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
NDUFAF1
NUSAP1
SPTBN5
CTDSPL2
DUOX1
DLL4
INO80
ZNF280D
TRPM7
PPP1R14D
HAUS2
RMDN3
DNAJC17
MNS1
MYO5C
FAM214A
PAK6
DTWD1
CASC5
STARD9
VPS18
SQRDL
ZNF106
RFX7
SPATA5L1
CHAC1
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
C15orf48
SPPL2A
ZFYVE19
CGNL1
FRMD5
DISP2
C15orf57
KNSTRN
BMF
SHF
DUOXA1
CHST14
CASC4
TGM7
CATSPER2
LEO1
PLA2G4E
TRIM69
C15orf43
C15orf65
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
DYX1C1
SPRED1
ADAL
EXD1
FSIP1
RHOV
FAM227B
UBR1
PATL2
PLA2G4F
LRRC57
LYSMD2
WDR72
SLC24A5
PRTG
PLA2G4D
GLDN
USP50
TEX9
C15orf52
TNFAIP8L3
SHC4
CTXN2
C15orf53
C15orf54
DUOXA2
EIF2AK4
UNC13C
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
MIR147B
ANKRD63
JMJD7
PLA2G4B
MIR1282
MIR4716
MIR4713
MIR4712

Genes in Wide Peak

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

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

Genes
ASPSCR1
MIR4525
RAB40B
snoU13\|ENSG00000238403.1
snoU13\|ENSG00000238947.1
DUS1L
PCYT2
SLC25A10
ARHGDIA
CD7
CSNK1D
SLC25A10
FASN
GCGR
UTS2R
GPS1
FOXK2
MAFG
P4HB
PDE6G
PYCR1
RAC3
RFNG
MRPL12
SECTM1
TBCD
SLC16A3
HGS
ALYREF
NARF
DCXR
ANAPC11
SIRT7
NPLOC4
WDR45B
FN3K
C17orf62
FN3KRP
OGFOD3
ZNF750
TSPAN10
PPP1R27
B3GNTL1
NOTUM
STRA13
LRRC45
MYADML2
NPB
CCDC57
HEXDC
METRNL
OXLD1
CCDC137
ARL16
FAM195B
TEX19

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.23.

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

Genes
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
SNORA73B
RNU6ATAC27P
RN7SL559P
SCARNA1
GPN2
ZDHHC18
RN7SL165P
RN7SL501P
snoU13\|ENSG00000238316.1
RN7SL679P
MIR1976
HMGN2
RN7SL490P
AIM1L
SH3BGRL3
ZNF593
SCARNA18\|ENSG00000252691.1
SCARNA17\|ENSG00000252190.1
MAN1C1
snoU13\|ENSG00000238889.1
SYF2
snoU13\|ENSG00000238986.1
RN7SL857P
snoU13\|ENSG00000238538.1
RN7SL24P
RN7SL532P
MIR3115
MIR4684
LINC00339
RN7SL186P
RN7SL768P
RN7SL386P
RN7SL421P
MIR1256
UBXN10
PLA2G2C
PLA2G2D
PLA2G5
RN7SL304P
PLA2G2E
snoU13\|ENSG00000239027.1
RN7SL277P
RN7SL85P
AKR7A2
AKR7A3
MIR1290
MIR4695
snoU13\|ENSG00000239020.1
PADI6
MIR3972
U1\|ENSG00000228549.2
MST1L
ESPNP
CROCCP2
U1\|ENSG00000233421.3
CROCCP3
C1orf134
ANO7P1
C1orf64
snoU13\|ENSG00000238818.1
DDI2
AGMAT
SCARNA21\|ENSG00000251866.1
C1orf195
SCARNA11\|ENSG00000253085.1
RNA5SP41
PRAMEF14
PRAMEF18
C1orf158
snoU13\|ENSG00000238771.1
RNU6ATAC18P
SNORA59A
SNORA70\|ENSG00000252969.1
MIR4632
RN7SL649P
C1orf167
DRAXIN
snoU13\|ENSG00000271794.1
TARDBP
RN7SL614P
DFFA
RN7SL721P
RN7SL731P
RN7SKP269
SLC25A33
RNA5SP40
GPR157
SCARNA16\|ENSG00000252404.1
RN7SL451P
SNORA77\|ENSG00000221083.1
RN7SL729P
TNFRSF9
snoU13\|ENSG00000239166.1
LINC00337
RN7SL574P
MIR551A
MEGF6
LINC00982
TTC34
C1orf222
TMEM240
RN7SL657P
TAS1R3
RNF223
FAM41C
FAM87B
OR4F5
FAM138A
DDX11L1
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFB
DVL1
E2F2
ECE1
EPHA2
ENO1
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
ZBTB48
HMGCL
HSPG2
HTR1D
HTR6
ID3
STMN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SKI
SLC2A5
SLC9A1
SRM
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
SNHG3
NR0B2
MMP23B
KCNAB2
FCN3
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
THEMIS2
H6PD
ISG15
PLCH2
CROCC
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
SPEN
KDM1A
WDTC1
EMC1
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
CELA3B
ICMT
PADI4
TMEM50A
STX12
CLIC4
CHD5
SZRD1
LDLRAP1
NOC2L
FBXO2
FBXO6
HSPB7
ARHGEF16
AHDC1
SMPDL3B
SSU72
UBIAD1
PADI1
WRAP73
SLC45A1
HP1BP3
CELA2B
SDF4
MRTO4
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
FBLIM1
MED18
PQLC2
CASZ1
CPSF3L
C1orf159
AURKAIP1
MRPL20
TMEM51
XKR8
ARHGEF10L
VPS13D
ATAD3A
TMEM57
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
MTFR1L
CTNNBIP1
C1orf63
AGTRAP
PITHD1
NIPAL3
SEPN1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
PLA2G2F
CEP85
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
PHACTR4
AUNIP
EFHD2
MMEL1
RSG1
MUL1
NOL9
LIN28A
LINC00115
MORN1
FAM110D
DHDDS
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
SESN2
ESPN
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
LZIC
TRIM63
C1orf170
SYTL1
IGSF21
KIAA2013
THAP3
STPG1
UBXN11
FBXO44
ATPIF1
FHAD1
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
KLHDC7A
VWA5B1
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
PHF13
CCDC27
C1orf213
PDIK1L
SLC2A7
CALML6
IFNLR1
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
ATAD3C
AKR7L
TTLL10
TMCO4
ZNF683
NPHP4
SLC25A34
C1orf174
KLHL17
TMEM52
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
SPATA21
AGRN
CATSPER4
GPR153
FAM132A
HES5
SMIM1
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF17
PRAMEF4
PRAMEF13
SH2D5
NCMAP
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
PRAMEF11
PRAMEF6
MINOS1
ANKRD65
PRAMEF7
MIR429
TMEM88B
C1orf233
C1orf200
PRAMEF19
PRAMEF20
LACTBL1
PRAMEF22
PRAMEF15
PRAMEF16
CDK11A
SLC35E2B
C1orf234
OR4F29
MIR4253
MIR1273D
MIR4252
MIR3917
MIR3675
APITD1
MIR4419A
MIR4425
MIR4689
MIR4418
MIR4417
MIR378F
MIR5697

Genes in Wide Peak

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

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

Genes
FKSG52
MIR582
PDE4D

Genes in Wide Peak

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

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

Genes
AKT1
TCL1A
TRIP11
GOLGA5
DICER1
TCL6
BCL11B
RNA5SP389
LINC00221
LINC00226
ADAM6
KIAA0125
IGHJ1
IGHJ2
IGHJ3
IGHJ4
IGHJ5
IGHJ6
IGHM
IGHD
IGHG3
IGHG1
IGHA1
IGHG2
IGHG4
IGHE
IGHA2
CRIP1
C14orf79
LINC00638
ZBTB42
C14orf144
RN7SL634P
LINC00637
SNORD51\|ENSG00000202275.1
APOPT1
SNORA28
LINC00605
LINC00677
snoU13\|ENSG00000238853.1
RN7SL546P
snoU13\|ENSG00000239061.1
RN7SL472P
LINC00524
U3\|ENSG00000206761.1
MEG9
MIR369
MIR377
MIR485
MIR134
MIR382
MIR381HG
MIR376A1
MIR376C
MIR380
MIR299
MIR379
SNORD113\|ENSG00000222185.1
SNORD112\|ENSG00000252009.1
SNORD113\|ENSG00000222095.1
SNORD113\|ENSG00000201710.1
SNORD113\|ENSG00000201036.1
SNORD113\|ENSG00000201500.1
SNORD113\|ENSG00000200150.1
SNORD112\|ENSG00000251918.1
SNORD112\|ENSG00000252144.1
SNORD112\|ENSG00000251949.1
SNORD112\|ENSG00000252873.1
SNORD112\|ENSG00000251769.1
MEG8
MIR433
MEG3
RN7SKP92
RN7SL523P
YY1
DEGS2
MIR342
CCNK
U6\|ENSG00000272439.1
RN7SL714P
RN7SL710P
LINC00618
RN7SKP108
snoU13\|ENSG00000238776.1
DKFZP434O1614
C14orf132
LINC00617
GLRX5
SCARNA13
SNHG10
MIR4506
SLC24A4
NDUFB1
U3\|ENSG00000200042.1
RN7SL506P
SNORA11B
LINC00642
RN7SKP255
RN7SKP107
SERPINA3
BDKRB1
BDKRB2
CALM1
SERPINA6
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO3
DYNC1H1
EIF5
EML1
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
MARK3
ATXN3
SERPINA5
SERPINA1
SERPINA4
PPP2R5C
LGMN
PSMC1
MOK
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
GPR68
DLK1
MTA1
RPS6KA5
BAG5
C14orf2
CDC42BPB
TCL1B
TECPR2
FBLN5
SIVA1
CYP46A1
PAPOLA
RCOR1
PACS2
PPP1R13B
KIF26A
TMEM251
GPR132
SERPINA10
EVL
GSKIP
CINP
ASB2
CPSF2
CDCA4
NRDE2
ATG2B
UBR7
SMEK1
BTBD7
TDP1
ZNF839
KCNK13
DDX24
UNC79
BEGAIN
PPP4R4
MOAP1
INF2
OTUB2
ZFYVE21
WDR25
LINC00341
CLMN
CATSPERB
RIN3
C14orf159
TMEM121
AMN
IFI27L2
SETD3
HHIPL1
C14orf142
FAM181A
BTBD6
EFCAB11
EXOC3L4
WDR20
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
PLD4
ADSSL1
TTC8
TC2N
SLC25A29
GSC
SERPINA12
PRIMA1
TTC7B
SYNE3
NUDT14
LINC00521
SERPINA11
C14orf177
SLC25A47
LINC00523
CEP170B
C14orf80
CCDC85C
SERPINA9
COX8C
ASPG
SERPINA13P
C14orf64
RTL1
TMEM179
C14orf180
MIR127
MIR136
MIR154
MIR203
CCDC88C
MIR323A
MIR337
MIR345
MIR370
MIR381
MIR431
MIR323B
MIR409
MIR412
MIR410
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
RD3L
TEX22
MIR539
MIR544A
MIR487B
MIR411
MIR654
MIR655
MIR656
MIR758
MIR770
MIR300
MIR541
MIR665
MIR543
MIR889
DIO3OS
MIR1197
MIR1193
MIR4309
MIR3173
MIR151B
MIR4710
MIR2392

Genes in Wide Peak

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

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

Genes
RNA5SP431
PIH1
WWOX

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q34.

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

Genes
BRAF
EZH2
SMO
KIAA1549
CREB3L2
LINC00689
MIR595
RN7SL142P
SHH
RN7SKP280
HTR5A
RN7SL845P
RN7SL811P
SNORA26\|ENSG00000212590.1
snoU13\|ENSG00000238557.1
RNA5SP250
FABP5P3
snoU13\|ENSG00000239045.1
RN7SL76P
MIR3907
MIR671
IQCA1P1
CDK5
SSPO
SNORD112\|ENSG00000252557.1
RN7SL521P
RNY1
RNY3
RNY4
RNY5
RN7SL569P
RN7SL72P
U3\|ENSG00000199370.1
RN7SL456P
RNA5SP249
RN7SL207P
RN7SKP174
RNU6ATAC40P
OR2A9P
OR2A20P
CTAGE15
RN7SL481P
RN7SL535P
OR6W1P
TRBV30
TRBC2
PRSS3P2
TRBV28
TRBV27
TRBV19
TRBV9
TRBV2
PRSS3P3
MOXD2P
OR9A1P
OR9A3P
AGK
U6\|ENSG00000271932.1
RN7SL771P
RNA5SP248
snoU13\|ENSG00000238868.1
RNA5SP247
KLRG2
LUC7L2
SNORA40\|ENSG00000252188.1
snoU13\|ENSG00000239123.1
SNORA51\|ENSG00000201465.1
snoU13\|ENSG00000238984.1
snoU13\|ENSG00000239145.1
RN7SKP223
SNORD81\|ENSG00000202023.1
snoU13\|ENSG00000238488.1
LUZP6
C7orf73
U6\|ENSG00000272393.1
SNORD46\|ENSG00000201009.1
MIR29B1
MIR29A
RNA5SP246
COPG2
MIR335
snoU13\|ENSG00000239044.1
snoU13\|ENSG00000238336.1
RNA5SP245
RNA5SP244
TSPAN33
snoU13\|ENSG00000238733.1
RN7SL306P
KCP
RN7SL81P
CALU
RNA5SP243
RNA5SP242
MIR593
MIR592
GPR37
AASS
RN7SKP277
AOC1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CASP2
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GRM8
MNX1
IMPDH1
INSIG1
IRF5
KCNH2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PRSS1
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ASIC3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
FAM3C
FASTK
ABCB8
PAXIP1
KLHDC10
NUP205
AHCYL2
TNPO3
HYAL4
CLEC5A
MKRN1
POT1
CNTNAP2
GIMAP2
OR2F1
SLC13A4
TPK1
SND1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
MRPS33
NUB1
TAS2R5
CHPF2
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
METTL2B
TRPV5
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
STRIP2
ESYT2
ZNF398
KMT2C
EXOC4
GALNT11
LRRC4
LMBR1
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
TTC26
JHDM1D
TMUB1
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
ADCK2
PLXNA4
ZC3HAV1L
CADPS2
CPA5
CEP41
ZBED6CL
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
SSMEM1
SVOPL
MTPN
LRGUK
ASB10
PRSS58
RNF32
ASB15
CLEC2L
C7orf55
IQUB
TMEM213
GIMAP8
CRYGN
ZNF425
ZNF746
ATP6V0E2
RBM33
GALNTL5
RNF133
GIMAP7
ZNF467
ZNF800
GIMAP1
C7orf33
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
FAM115C
ZNF775
ATG9B
TAS2R60
BLACE
CTAGE6
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
WDR86
GSTK1
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A42
MIR182
MIR183
MIR96
AKR1B15
CTAGE15
OR2A2
LMOD2
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
ACTR3C
TMEM229A
CTAGE4
CTAGE8
SMKR1
ZNF783
MIR548F4
MTRNR2L6
TMEM178B
MIR4468
MIR5707

Genes in Wide Peak

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

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

Genes
RN7SL695P
SMAD4
ELAC1

Genes in Wide Peak

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

Table S46. 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 Xq21.33.

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

Genes
SNORA25\|ENSG00000252296.1
RN7SL74P
RPA4

Genes in Wide Peak

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

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

Genes
BCL9
NOTCH2
NRAS
PDE4DIP
TRIM33
RBM15
HIST2H3A
HIST2H2AA3
HIST2H3C
FAM72C
FCGR1C
RNA5SP59
NBPF15
RNA5SP58
NBPF24
RN7SL261P
ACP6
LINC00624
HYDIN2
RNA5SP57
PDZK1P1
RNF115
NUDT17
GNRHR2
NBPF10
SEC22B
RN7SKP88
LINC00623
NBPF8
SRGAP2B
ANKRD20A12P
FCGR1B
HIST2H2BA
LINC00622
snoU13\|ENSG00000238679.1
RNA5SP56
WDR3
SNORA40\|ENSG00000212266.1
MAN1A2
MIR942
TTF2
RNA5SP55
MIR548AC
ATP1A1OS
U3\|ENSG00000221040.1
SNORA42\|ENSG00000207502.1
RN7SL420P
RN7SL432P
DENND2C
BCL2L15
LRIG2
snoU13\|ENSG00000238975.1
WNT2B
snoU13\|ENSG00000238761.1
snoU13\|ENSG00000239111.1
ATP5F1
PGCP1
DENND2D
RNA5SP54
CYMP
SNORA25\|ENSG00000200536.1
ALX3
RNU6V
GNAI3
KIAA1324
SCARNA2
TMEM167B
TAF13
SPATA42
NBPF5P
SLC25A24P1
RN7SKP285
snoU13\|ENSG00000238296.1
SCARNA16\|ENSG00000252765.1
DPH5
MIR553
LPPR5
RN7SKP270
RN7SL831P
ALG14
snoU13\|ENSG00000238389.1
RN7SL440P
ARHGAP29
GCLM
DNTTIP2
RNA5SP53
DR1
RN7SKP123
RN7SL692P
SNORA51\|ENSG00000207022.1
SNORA66\|ENSG00000207523.1
SNORA66\|ENSG00000251795.1
SNORD21
RN7SL824P
RPAP2
ACTBP12
RN7SL235P
RN7SL653P
BARHL2
U3\|ENSG00000199666.1
ABCA4
ADORA3
AGL
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CNN3
COL11A1
CSF1
DBT
DPYD
S1PR1
CELSR2
EXTL2
F3
FCGR1A
FMO5
GFI1
GJA5
GJA8
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
HMGCS2
HSD3B1
HSD3B2
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PDZK1
PRKAB2
PSMA5
PTGFRN
ABCD3
RAP1A
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TBX15
TGFBR3
TSHB
VCAM1
CSDE1
EVI5
CDC7
HIST2H2AC
HIST2H2BE
HIST2H4A
BCAR3
ITGA10
CDC14A
RTCA
PEX11B
SLC16A4
CD101
CHD1L
LPPR4
SV2A
RBM8A
TSPAN2
BCAS2
WARS2
CEPT1
PIAS3
VAV3
LAMTOR5
POLR3C
TXNIP
AP4B1
PHTF1
AHCYL1
ADAM30
CD160
GLMN
DDX20
MTF2
NTNG1
WDR47
CLCC1
KIAA1107
SLC35A3
NBPF14
RWDD3
PTPN22
PHGDH
CHIA
GPSM2
SLC25A24
TMED5
BOLA1
HAO2
SNX7
GPR89B
GPR88
TRMT13
RSBN1
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
PRMT6
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
OLFML3
AMIGO1
PTBP2
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
SIKE1
TRIM45
VANGL1
GPR61
REG4
ZNF644
POLR3GL
PROK1
PSRC1
STRIP1
ZNF697
HENMT1
OLFM3
MAB21L3
SLC44A3
ATXN7L2
C1orf194
LRRC39
LIX1L
DRAM2
PIFO
C1orf162
SYT6
TMEM56
NBPF4
HFE2
ANKRD35
SLC30A7
NBPF12
CHIAP2
FNDC7
SASS6
PPIAL4A
HFM1
UBL4B
NBPF11
SPAG17
HIPK1
EPHX4
AKNAD1
MAGI3
FAM19A3
NBPF16
FAM102B
SYPL2
CYB561D1
ANKRD34A
BTBD8
HIST2H2AB
PPM1J
CCDC18
MYBPHL
C1orf146
FAM69A
SLC6A17
C1orf137
NOTCH2NL
FRRS1
NBPF9
MIR197
HIST2H2BF
HIST2H4B
PPIAL4G
PPIAL4D
NBPF6
PPIAL4B
GPR89A
PPIAL4C
HIST2H3D
FAM72B
HIST2H2AA4
FAM72D
GPR89C
MIR760
NBPF20
MIR320B1
MIR378G
MIR137HG

Genes in Wide Peak

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

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

Genes
RN7SL741P
RN7SL289P
PABPC3
LSP1\|ENSG00000269099.1
TPTE2P1
RNY1P7
TPTE2P6
LINC00566
MIR2276
ANKRD20A19P
LINC00352
LINC00327
LINC00362
RNY3P4
LINC00621
SNORD36\|ENSG00000253094.1
LINC00424
RN7SL766P
snoU13\|ENSG00000238878.1
ZDHHC20
RNA5SP25
MIPEPP3
ESRRAP2
RN7SL80P
SNORD27\|ENSG00000252128.1
snoU13\|ENSG00000238893.1
HNRNPA1P30
MIR4499
LINC00556
snoU13\|ENSG00000238665.1
RN7SL166P
PSPC1
LINC00350
LINC00421
TUBA3C
RNA5SP24
LINC00442
PHF2P2
LINC00387
LINC00388
LINC00349
PARP4
ATP12A
FGF9
GJA3
GJB2
MIPEP
SGCG
ZMYM2
IFT88
MTMR6
ZMYM5
NUPL1
SAP18
GJB6
SACS
LATS2
CRYL1
IL17D
MPHOSPH8
TNFRSF19
CENPJ
RNF17
XPO4
MRP63
TPTE2
AMER2
N6AMT2
SKA3
MICU2
SPATA13
C1QTNF9
C1QTNF9B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q11.2.

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

Genes
CYLD
HERPUD1
RN7SL143P
SLC38A7
snoU13\|ENSG00000239121.1
SNORA50\|ENSG00000206952.2
SNORA46\|ENSG00000207493.1
RN7SL645P
TEPP
MT1DP
MT1M
MT1E
MT1L
MT2A
OGFOD1
MIR3935
IRX6
RN7SL841P
CRNDE
FTO
RNA5SP427
snoU13\|ENSG00000238645.1
CASC16
LINC00919
RN7SKP142
HNRNPA1P48
RNA5SP426
NKD1
SNORD112\|ENSG00000252077.1
snoU13\|ENSG00000238544.1
SNORA70\|ENSG00000252526.1
RNY4P3
snoU13\|ENSG00000239038.1
snoU13\|ENSG00000239013.1
RN7SL54P
LONP2
RNA5SP425
RNA5SP424
ITFG1
snoU13\|ENSG00000238834.1
MYLK3
VPS35
ANKRD26P1
RNA5SP423
RNA5SP422
RNA5SP421
RNA5SP420
RNA5SP419
RNA5SP418
RNA5SP417
RNA5SP416
RNA5SP415
RNA5SP413
RNA5SP410
RNA5SP409
RNA5SP408
RNA5SP407
RNA5SP406
LINC00273
ARHGAP23P1
HERC2P8
HERC2P5
TP53TG3
TP53TG3D
HERC2P4
ADCY7
AMFR
BBS2
CBLN1
CES1
CETP
CNGB1
CSNK2A2
GNAO1
GOT2
KIFC3
MMP2
MMP15
MT1A
MT1B
MT1F
MT1G
MT1H
MT1JP
MT1X
MT3
PHKB
POLR2C
RBL2
SALL1
CCL17
CCL22
CX3CL1
SIAH1
SLC6A2
SLC12A3
GPR56
N4BP1
NUP93
IRX5
DNAJA2
KATNB1
ZNF267
NUDT21
CNOT1
ZNF423
RPGRIP1L
ARL2BP
ORC6
TOX3
CCDC113
C16orf80
BRD7
PLLP
CES1P1
LPCAT2
HEATR3
DOK4
COQ9
CIAPIN1
ZNF319
NOD2
PAPD5
AKTIP
GINS3
NDRG4
IRX3
USB1
SHCBP1
SETD6
FAM192A
CHD9
NETO2
NLRC5
CCDC135
CAPNS2
MT4
GPT2
ABCC11
RSPRY1
CCDC102A
ABCC12
C16orf78
SNX20
CPNE2
GPR114
PRSS54
CES5A
GPR97
CNEP1R1
SLC6A10P
C16orf87
C16orf97
TP53TG3C
TP53TG3B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.1.

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

Genes
FAM167A

Genes in Wide Peak

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

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

Genes
PPP2R1A
ERCC2
KLK2
TFPT
ZNF331
RN7SL525P
RN7SL693P
RNA5SP473
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
ZNF137P
MIR643
snoU13\|ENSG00000238630.1
HCCAT3
FPR1
snoU13\|ENSG00000238486.1
SIGLEC5
CEACAM18
SIGLEC22P
SIGLEC17P
KLK13
KLK9
KLKP1
SNORD88C
SNORD88A
SNORD88B
LRRC4B
SPIB
RN7SL324P
NAPSB
SIGLEC16
U3\|ENSG00000221125.1
MIR4751
MIR4750
MIR4749
ADM5
MIR5088
BCL2L12
SNORD35B
SNORD35A
SNORD34
SNORD33\|ENSG00000199631.1
SNORD32A
MIR4324
RN7SL708P
RN7SL345P
SEC1P
DBP
GRWD1
C19orf68
CABP5
TPRX2P
SNORD23\|ENSG00000221803.1
RN7SL322P
RN7SL533P
snoU13\|ENSG00000252071.1
MIR320E
RN7SL364P
PGLYRP1
NOVA2
MIR642A
RN7SL836P
MIR330
PPM1N
A1BG
AP2A1
KLK3
BAX
BCAT2
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CGB
AP2S1
CRX
DMPK
DMWD
EMP3
ERCC1
ETFB
FCAR
FCGRT
FLT3LG
FOSB
FPR2
FPR3
FTL
FUT1
FUT2
GIPR
GPR4
GPR32
GRIN2D
ARHGAP35
GYS1
HAS1
FOXA3
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LHB
LIG1
LIM2
MYBPC2
NKG7
CNOT3
NPAS1
NTF4
NUCB1
PEG3
POLD1
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PTGIR
PTPRH
RPL18
RPL28
RPS5
RPS9
RPS11
RRAS
RTN2
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPD2
SPIB
AURKC
SULT2B1
SULT2A1
TNNI3
TNNT1
TULP2
NR1H2
VASP
ZNF8
ZNF17
ZNF28
MZF1
ZNF132
ZNF135
ZNF154
ZNF175
SYMPK
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
UBE2M
CYTH2
NCR1
NAPSA
KLK4
ZNF432
DHX34
SAE1
TRIM28
ZNF256
LILRB2
ZNF211
TRAPPC2P1
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
KPTN
KLK8
PNKP
U2AF2
ATF5
PPP6R1
CARD8
ZC3H4
FBXO46
RPL13A
SYNGR4
LILRA4
ZIM2
NUP62
HSPBP1
PPP1R15A
EML2
ZNF324
KLK5
PRKD2
ZNF473
CCDC9
PRPF31
IRF2BP1
FGF21
SIGLEC7
BBC3
DKKL1
SIGLEC9
SIGLEC8
C5AR2
CHMP2A
DHDH
ZNF544
UBE2S
SLC6A16
STRN4
EPN1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF581
PTOV1
PPP1R12C
TRPM4
ZNF586
QPCTL
FAM83E
EPS8L1
RASIP1
TMEM160
PIH1D1
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
SPHK2
MEIS3
SLC17A7
NAT14
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
USP29
PLEKHA4
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
ELSPBP1
LIN7B
HIF3A
ZNF649
ZSCAN18
RPL23AP79
TSEN34
MBOAT7
FKRP
ZSCAN5A
ZNF329
TBC1D17
ZNF419
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
ZNF702P
ZNF606
ZNF614
FUZ
OPA3
RSPH6A
ZNF611
MED25
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
ZNF347
ZNF577
SUV420H2
C19orf48
ZBTB45
ZNF587
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
ZNF551
ZNF616
ZNF766
ZNF468
ZNF160
CTU1
ZNF835
ZNF765
NLRP12
MYADM
ZNF845
CCDC114
ACPT
CGB5
CGB7
LENG9
CGB8
GNG8
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
KIR3DL3
ZNF837
CLDND2
ZNF816
ZNF543
COX6B2
OSCAR
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
VSIG10L
LINC00085
ZNF480
ZNF534
ZNF578
C19orf18
ZNF418
KLC3
TMEM190
TMC4
TPM3P9
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF836
ZNF610
ZNF320
ZNF497
ZNF550
ZNF579
ZNF114
ZNF525
SPACA4
NLRP7
ZNF584
ZSCAN4
NLRP11
TMEM86B
PRR24
ZNF549
IL4I1
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
TPRX1
MAMSTR
IZUMO1
EMC10
KLK9
SIGLECL1
ZNF615
ZNF841
VSTM1
TMEM150B
FAM71E2
VN1R2
VN1R4
NLRP9
MYPOP
NANOS2
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
ZNF530
DNAAF3
LILRA5
IGFL1
ZNF773
IGFL3
ZNF808
ZNF470
ZNF749
ZNF324B
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
TARM1
MIR371A
MIR372
MIR373
IGFL4
DPRX
ASPDH
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
CCDC61
SHISA7
MIR769
SIGLEC14
SGK110
BSPH1
ZNF587B
MIR1323
MIR3191
PPP5D1
ZNF865
MIR4754
MIR4752

Genes in Wide Peak

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

Table S53. 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 6p24.2.

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

Genes
IRF4
DEK
HIST1H2BC
HIST1H4C
snoU13\|ENSG00000238322.1
RNY5P5
CMAHP
RN7SL334P
C6orf62
SNORD46\|ENSG00000251830.1
RN7SKP240
LINC00340
RN7SL128P
MBOAT1
ID4
RNA5SP205
snoU13\|ENSG00000238458.1
RNA5SP204
STMND1
U3\|ENSG00000251793.1
MIR4639
RN7SL332P
NOL7
RN7SKP204
PHACTR1
RN7SKP293
SNORA67\|ENSG00000207419.1
snoU13\|ENSG00000238896.1
RNA5SP203
C6orf52
GCNT6
LINC00518
RNU6ATAC21P
OFCC1
HULC
snoU13\|ENSG00000251762.1
RN7SL554P
LY86
RN7SL221P
MIR3691
RMRPP2
snoU13\|ENSG00000238801.1
RNA5SP202
snoU13\|ENSG00000252668.1
C6ORF50
RNA5SP201
C6orf195
RN7SL352P
snoU13\|ENSG00000238438.1
BMP6
BPHL
DSP
E2F3
EDN1
SERPINB1
F13A1
FOXF2
FOXC1
GCNT2
GMDS
GMPR
GPLD1
HIST1H1C
HIST1H1E
HIST1H1T
HIST1H2BD
HIST1H2BB
HIST1H1A
HFE
HIVEP1
JARID2
MAK
NEDD9
NQO2
SERPINB6
SERPINB9
PRL
RREB1
ATXN1
SLC17A1
SOX4
SSR1
TFAP2A
TPMT
TUBB2A
ALDH5A1
HIST1H2AC
HIST1H2AB
HIST1H3A
HIST1H3C
HIST1H3B
HIST1H4A
HIST1H4B
RIPK1
PRPF4B
GCM2
CD83
CDYL
EEF1E1
FAM65B
KIAA0319
NUP153
RANBP9
SLC17A4
SLC17A2
ECI2
TRIM38
CAP2
SCGN
FARS2
SLC17A3
RPP40
SIRT5
FAM50B
MYLIP
SLC35B3
GMNN
TBC1D7
NRN1
FAM8A1
DCDC2
TMEM14C
TDP2
GFOD1
ELOVL2
CDKAL1
PAK1IP1
LRRC16A
EXOC2
ACOT13
WRNIP1
DUSP22
LYRM4
MRS2
SLC22A23
BLOC1S5
MCUR1
KIF13A
TXNDC5
TMEM14B
RIOK1
DTNBP1
ADTRP
FOXQ1
HUS1B
NRSN1
SNRNP48
HDGFL1
HIST1H2AA
KDM1B
RBM24
RNF182
SMIM13
SYCP2L
PXDC1
FAM217A
RNF144B
HIST1H2BA
CAGE1
MYLK4
TUBB2B
KAAG1
NHLRC1
PSMG4
C6orf201
PPP1R3G
MIR548A1
TMEM170B
MIR4645
MIR5689
MIR5683

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
MAP2K4
MIR744

Genes in Wide Peak

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

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

Genes
CARS
FANCF
HRAS
LMO1
NUP98
LINC00678
RNA5SP339
SVIP
RNA5SP338
RNA5SP337
RNA5SP336
SLC6A5
SNORA1\|ENSG00000207407.1
MIR4486
RNA5SP335
RNA5SP334
RNA5SP333
SAA3P
TPH1
SNORD14B
SNORD14A
OR7E14P
RN7SKP90
C11orf58
RN7SL188P
PSMA1
RNA5SP332
SPON1
RNA5SP331
RN7SKP151
LINC00958
SCARNA16\|ENSG00000252329.1
PARVA
SNORD97
LYVE1
RNU6ATAC33P
ADM
RN7SKP50
RN7SL56P
snoU13\|ENSG00000238387.1
SNORA23
MIR5691
RNA5SP330
SNORA45
SNORA3\|ENSG00000200983.1
SCARNA20\|ENSG00000252778.1
OR10AB1P
GVINP1
TAF10
RRP8
TIMM10B
RNA5SP329
TRIM34
OR51J1
OR51B5
HBG1
HBBP1
OR52A4
OR51H1P
SNORA62\|ENSG00000201980.1
OR51C1P
SNORA7\|ENSG00000206976.1
snoU13\|ENSG00000238686.1
TRPC2
TSSC2
SNORA54
SLC22A18AS
KCNQ1OT1
RPL26P30
C11orf21
MIR483
H19
C11orf89
FAM99B
MOB2
MUC5AC
SNORA52
RPLP2
TMEM80
SCT
MIR210HG
RN7SL838P
ODF3
AP2A2
AMPD3
APBB1
RHOG
ARNTL
ART1
ASCL2
BDNF
CALCA
CALCB
CCKBR
CD81
CD151
CDKN1C
TPP1
CNGA4
COPB1
CTSD
DRD4
DUSP8
EIF4G2
GAS2
GTF2H1
HBB
HBD
HBE1
HBG2
HPX
IGF2
ILK
INS
IRF7
KCNC1
KCNJ11
KCNQ1
LDHA
LDHC
LSP1\|ENSG00000130592.9
MUC2
MUC6
MYOD1
NAP1L4
NELL1
NUCB2
SLC22A18
PDE3B
PIK3C2A
POLR2L
PSMA1
PSMD13
PTH
RNH1
MRPL23
RPL27A
RPS13
RRM1
SAA1
SAA2
SAA4
SMPD1
TRIM21
ST5
STIM1
ABCC8
TALDO1
TEAD1
TH
TSPAN4
TNNI2
TNNT3
TSG101
PHLDA2
TUB
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
CSRP3
BBOX1
PPFIBP2
IFITM1
OR6A2
DCHS1
EIF3F
BRSK2
MICAL2
CTR9
TRIM66
TSPAN32
TSSC4
USH1C
PRMT3
MRVI1
TRIM22
IFITM3
DEAF1
IPO7
HTATIP2
IFITM2
TRIM3
PKP3
HPS5
RRAS2
SWAP70
DENND5A
SIRT3
OR52A1
ARFIP2
SERGEF
OR10A3
TIMM10B
DKK3
RBMXL2
PGAP2
TRPM5
UBQLN3
RNF141
BET1L
CEND1
CYB5R2
CDHR5
TOLLIP
ZDHHC13
USP47
TRIM68
UEVLD
LIN7C
LGR4
PIDD
KCNQ1DN
SOX6
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
CHRNA10
SLC17A6
PNPLA2
PHRF1
SCUBE2
ZBED5
SIGIRR
RIC8A
MRPL17
ANO3
EPS8L2
STK33
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
E2F8
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
SBF2
KIF18A
FAM160A2
FAR1
BTBD10
PTPN5
MICALCL
TRIM5
NAV2
SYT8
CCDC34
PRKCDBP
SAAL1
OSBPL5
LRRC56
MRGPRE
ART5
MRGPRX2
MRGPRX3
MRGPRX4
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR5P2
OR5P3
CYP2R1
DBX1
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
MUC15
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
SLC5A12
LDHAL6A
C11orf42
NLRP6
OR56B4
ANO5
OR52B2
C11orf35
OR51F1
MRGPRX1
CSNK2A3
OR51V1
EFCAB4A
IGSF22
OR10A4
OLFML1
NLRP10
NLRP14
ANO9
LUZP2
B4GALNT4
OR52L1
OR2AG2
OR52B6
OTOG
OR10A2
OVCH2
PDDC1
GALNT18
NCR3LG1
MRGPRG
IFITM5
FAM99A
OR56B1
INSC
FIBIN
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR10A6
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
TMEM41B
MIR610
MUC5B
MIR302E
MIR3159
MIR4298
MIR4299
MTRNR2L8
CCDC179
MIR4686
MIR4694
MIR4687

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q21.3.

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

Genes
PTPN13

Genes in Wide Peak

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

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

Genes
RN7SL872P
RNA5SP251
RPL23AP53
OR4F21
CLN8
MYOM2
DLGAP2
ARHGEF10
KBTBD11
FBXO25
TDRP
ERICH1
ZNF596
MIR596

Genes in Wide Peak

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

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

Genes
SNORA70\|ENSG00000207098.1
C21orf62
C21orf49
C21ORF59
TCP10L
LINC00846
RNA5SP490
SNORA33\|ENSG00000252045.1
SNORA80
RN7SL109P
LINC00159
SNORA81\|ENSG00000238390.1
LINC00307
snoU13\|ENSG00000239171.1
LINC00189
U3\|ENSG00000212479.1
RWDD2B
N6AMT1
LINC00113
LINC00515
snoU13\|ENSG00000238314.1
RNA5SP489
7SK\|ENSG00000232512.2
RN7SL609P
LINC00308
LINC00317
LINC00320
RN7SKP147
RN7SL163P
SNORD74\|ENSG00000201025.1
snoU13\|ENSG00000238591.1
RNA5SP488
ANKRD20A11P
CYP4F29P
ANKRD30BP2
BAGE2
SNORA70\|ENSG00000252199.1
RN7SL52P
TEKT4P2
MIR3648
APP
ATP5J
CXADR
GABPA
GRIK1
NCAM2
TMPRSS15
SOD1
HSPA13
TIAM1
TPTE
NRIP1
SYNJ1
CLDN8
ADAMTS1
URB1
USP16
CCT8
BTG3
ADAMTS5
LTN1
CLDN17
USP25
HUNK
RBM11
MIS18A
LINC00158
MRPL39
C21orf91
MRAP
C21orf59
MAP3K7CL
SCAF4
JAM2
EVA1C
SAMSN1
C21orf119
PAXBP1
CYYR1
LINC00161
CHODL
LIPI
ABCC13
LINC00314
POTED
LINC00478
MIRLET7C
MIR125B2
MIR155HG
MIR99A
BACH1
MIR4327
MIR548X
MIR3687
C21orf37
MIR4759

Genes in Wide Peak

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

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

Genes
RN7SKP148
HRH2

Arm-level results

Table 3. Get Full Table Arm-level significance table - 25 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	0.32	6.83	4.44e-11	0.06	-3.99	1
1q	1195	0.48	13.8	0	0.08	-3.02	1
2p	624	0.22	1.08	0.573	0.09	-3.97	1
2q	967	0.12	-2.62	1	0.16	-0.999	1
3p	644	0.25	1.95	0.128	0.43	9.04	0
3q	733	0.58	15.8	0	0.28	2.66	0.0108
4p	289	0.07	-4.55	1	0.46	10.3	0
4q	670	0.08	-4.16	1	0.33	5.81	2.1e-08
5p	183	0.37	5.89	1.29e-08	0.18	-1.1	1
5q	905	0.15	-1.56	1	0.23	2.03	0.051
6p	710	0.19	-0.00652	1	0.21	0.642	0.509
6q	556	0.15	-1.81	1	0.29	3.78	0.000355
7p	389	0.14	-2.82	1	0.10	-4.08	1
7q	783	0.14	-2.19	1	0.15	-1.66	1
8p	338	0.22	0.465	1	0.36	5.71	3.37e-08
8q	551	0.33	5.22	5.22e-07	0.13	-2.52	1
9p	301	0.19	-0.824	1	0.23	0.784	0.467
9q	700	0.19	-0.318	1	0.21	0.719	0.484
10p	253	0.10	-4.14	1	0.25	1.45	0.167
10q	738	0.07	-4.65	1	0.27	3.36	0.00146
11p	509	0.05	-5.43	1	0.35	6.19	2.43e-09
11q	975	0.04	-4.78	1	0.40	9.61	0
12p	339	0.21	-0.0868	1	0.17	-1.71	1
12q	904	0.17	-0.528	1	0.07	-4.7	1
13q	560	0.11	-3.25	1	0.30	3.91	0.00024
14q	938	0.17	-0.375	1	0.15	-1.45	1
15q	810	0.21	0.696	0.907	0.20	0.302	0.679
16p	559	0.17	-1.28	1	0.14	-2.57	1
16q	455	0.15	-2.04	1	0.18	-1.03	1
17p	415	0.09	-4.12	1	0.36	6.3	1.51e-09
17q	972	0.16	-1.07	1	0.15	-1.2	1
18p	104	0.19	-0.98	1	0.23	0.473	0.593
18q	275	0.14	-2.64	1	0.28	2.68	0.0108
19p	681	0.15	-1.8	1	0.27	3.11	0.00319
19q	935	0.23	1.91	0.128	0.18	-0.0857	0.912
20p	234	0.36	5.93	1.23e-08	0.13	-3	1
20q	448	0.40	7.98	1.06e-14	0.07	-4.49	1
21q	258	0.15	-2.42	1	0.19	-0.93	1
22q	564	0.13	-2.64	1	0.27	2.73	0.0101
Xp	418	0.11	-3.41	1	0.30	3.76	0.000355
Xq	668	0.15	-1.63	1	0.25	2.37	0.0225

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/CESC-TP/19075895/GDAC_MergeDataFiles_12183216/CESC-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt
Markers File = /xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt
Reference Genome = /xchip/cga/reference/gistic2/hg19_GENCODE_v18_20140127.mat
CNV Files = /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.txt
Amplification Threshold = 0.1
Deletion Threshold = 0.1
Cap Values = 1.5
Broad Length Cutoff = 0.7
Remove X-Chromosome = 0
Confidence Level = 0.99
Join Segment Size = 4
Arm Level Peel Off = 1
Maximum Sample Segments = 2000
Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 295 Input Tumor Samples.

Tumor Sample Names
TCGA-2W-A8YY-01A-11D-A37M-01
TCGA-4J-AA1J-01A-21D-A386-01
TCGA-BI-A0VR-01A-11D-A10T-01
TCGA-BI-A0VS-01A-11D-A10T-01
TCGA-BI-A20A-01A-11D-A14V-01
TCGA-C5-A0TN-01A-21D-A14V-01
TCGA-C5-A1BE-01B-11D-A13V-01
TCGA-C5-A1BF-01B-11D-A13V-01
TCGA-C5-A1BI-01B-11D-A13V-01
TCGA-C5-A1BJ-01A-11D-A13V-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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