SNP6 Copy number analysis (GISTIC2)

Uterine Carcinosarcoma (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/C1QF8S7R

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 56 tumor samples used in this analysis: 21 significant arm-level results, 25 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 - 25 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband	Q value	Residual Q value	Wide Peak Boundaries	# Genes in Wide Peak
19q12	1.4274e-21	1.4274e-21	chr19:30712323-30831808	1
3q26.2	4.8739e-09	4.8739e-09	chr3:168526502-168814908	2
4p16.3	1.4214e-07	1.4214e-07	chr4:1792019-1870419	2
1q22	3.1905e-06	3.1905e-06	chr1:155870519-156017401	8
20q11.21	2.0971e-12	5.9148e-06	chr20:30535307-30921748	12
20q11.21	3.6e-10	0.00027345	chr20:29983442-30369453	12
8p11.21	4.6343e-06	0.00053433	chr8:42725564-47463861	10
8q11.23	4.1938e-06	0.00089729	chr8:48357987-57188018	42
19p13.2	0.0014153	0.0014153	chr19:10492041-10767789	12
8q24.21	2.2187e-08	0.0024551	chr8:129548135-129565078	0 [RN7SKP226]
6p24.2	0.0026462	0.0026462	chr6:11367262-11448879	1
13q31.3	0.0026462	0.0026462	chr13:90659392-96245151	26
8q24.21	8.9908e-06	0.0029578	chr8:128630217-129102510	5
16p11.2	0.0039776	0.0039776	chr16:30907404-30943981	2
17q25.1	0.00067137	0.0045262	chr17:73581977-73757386	7
10q22.2	0.0058757	0.0058757	chr10:76500842-77828069	9
11q13.1	0.0085652	0.0085652	chr11:63669372-63995301	11
3p25.1	0.010149	0.010149	chr3:13643232-13895816	3
17q12	0.0046324	0.033763	chr17:37822312-37969982	8
5p13.2	0.047229	0.047229	chr5:36321031-36701657	2
Xp11.21	0.04875	0.04875	chrX:55567455-56241386	3
2q13	0.079059	0.079059	chr2:113940840-114236564	3
12q12	0.069456	0.10753	chr12:44445547-46909264	11
12q15	0.049549	0.1956	chr12:69164647-71445992	17
2p14	0.22141	0.22141	chr2:68076781-68330783	1

Genes in Wide Peak

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

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

Genes
ZNF536

Genes in Wide Peak

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

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

Genes
EGFEM1P
MECOM

Genes in Wide Peak

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

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

Genes
FGFR3
LETM1

Genes in Wide Peak

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

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

Genes
SCARNA4\|ENSG00000252808.1
SNORA42\|ENSG00000207475.1
RIT1
SSR2
ARHGEF2
KIAA0907
UBQLN4
RXFP4

Genes in Wide Peak

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

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

Genes
RNA5SP482
RNA5SP481
XKR7
HCK
PLAGL2
KIF3B
TM9SF4
POFUT1
PDRG1
TSPY26P
CCM2L
MIR1825

Genes in Wide Peak

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

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

Genes
LINC00028
DEFB122
BCL2L1
ID1
TPX2
REM1
HM13
COX4I2
DEFB121
DEFB123
DEFB124
MIR3193

Genes in Wide Peak

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

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

Genes
HOOK3
RN7SKP41
U3\|ENSG00000201329.1
POTEA
RN7SL806P
FNTA
RNF170
SGK196
HGSNAT
MIR4469

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q11.23.

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

Genes
PLAG1
TCEA1
CHCHD7
SNORA3\|ENSG00000221093.1
SNORD54
RPS20
RN7SL323P
RN7SL798P
SNORA1\|ENSG00000199405.1
RNA5SP265
XKR4
RN7SL250P
RNU105C
RNU6ATAC32P
MRPL15
NPBWR1
SNORA7\|ENSG00000201316.1
RN7SKP294
UBE2V2
CEBPD
LYN
MCM4
MOS
OPRK1
PRKDC
RP1
SNAI2
RGS20
ST18
RB1CC1
LYPLA1
SPIDR
ATP6V1H
SNTG1
SOX17
EFCAB1
TGS1
PCMTD1
TMEM68
PXDNL
FAM150A
C8orf22

Genes in Wide Peak

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

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

Genes
MIR1238
MIR1181
CDKN2D
ILF3
PDE4A
KEAP1
AP1M2
CDC37
S1PR5
SLC44A2
KRI1
ATG4D

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p24.2.

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

Genes
NEDD9

Genes in Wide Peak

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

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

Genes
RNY4P27
RNY3P8
snoU13\|ENSG00000238463.1
LINC00557
LINC00391
RN7SL585P
RNA5SP36
RNA5SP35
SNORD22
MIR548AS
RNU4ATAC3P
LINC00379
LINC00410
RNA5SP34
LINC00559
DCT
GPC5
CLDN10
GPC6
ABCC4
SOX21
DZIP1
TGDS
GPR180
MIR17HG
MIR622

Genes in Wide Peak

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

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

Genes
MYC
TMEM75
MIR1205
MIR1207
PVT1

Genes in Wide Peak

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

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

Genes
CTF1
FBXL19

Genes in Wide Peak

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

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

Genes
MYO15B
GALK1
ITGB4
RECQL5
SAP30BP
SMIM5
SMIM6

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q22.2.

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

Genes
MIR606
VDAC2
KAT6B
DUSP13
C10orf11
ZNF503
COMTD1
SAMD8
DUPD1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.1.

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

Genes
OTUB1
COX8A
MARK2
STIP1
FLRT1
MACROD1
NAA40
FERMT3
TRPT1
NUDT22
RCOR2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3p25.1.

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

Genes
WNT7A
LINC00620
FBLN2

Genes in Wide Peak

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

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

Genes
ERBB2
IKZF3
MIR4728
PNMT
TCAP
GRB7
MIEN1
PGAP3

Genes in Wide Peak

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

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

Genes
RNA5SP181
SLC1A3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp11.21.

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

Genes
SNORD112\|ENSG00000252961.1
RRAGB
FOXR2

Genes in Wide Peak

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

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

Genes
PAX8
PSD4
CBWD2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q12.

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

Genes
SCAF11
RN7SL246P
RNA5SP361
NELL2
PLEKHA8P1
SLC38A2
SLC38A1
TMEM117
ANO6
ARID2
DBX2

Genes in Wide Peak

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

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

Genes
MDM2
MYRFL
RN7SL804P
SLC35E3
CPM
LYZ
CNOT2
PTPRB
PTPRR
YEATS4
CCT2
FRS2
CPSF6
KCNMB4
RAB3IP
BEST3
LRRC10

Genes in Wide Peak

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

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

Genes
C1D

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
19p13.3	1.9441e-13	1.9441e-13	chr19:1-1107034	43
15q15.1	5.2724e-10	1.1081e-07	chr15:38991457-40735548	21
3q13.31	1.6679e-07	1.6679e-07	chr3:116297365-118620828	4
5q12.1	2.7405e-07	2.7405e-07	chr5:58151172-59818245	3
3p14.2	1.0092e-05	1.0092e-05	chr3:52578475-61547330	69
Xp21.1	1.3389e-05	1.3389e-05	chrX:32117084-32611359	2
2q22.1	2.739e-05	2.739e-05	chr2:140708948-143637838	2
12q23.1	6.8898e-05	0.00012509	chr12:99476105-100107912	2
16q23.1	0.00022661	0.00023177	chr16:78098006-79299841	3
4q22.1	0.00016044	0.00028298	chr4:90844993-93240505	2
13q14.2	5.8942e-05	0.00036226	chr13:48875329-49152025	3
22q13.31	0.00146	0.0015167	chr22:41958863-51304566	130
20p12.1	0.0045867	0.0044677	chr20:14301156-16252980	2
8p23.2	0.0048239	0.0048239	chr8:1-29193438	234
1p36.21	0.0056975	0.0056975	chr1:1-28700785	477
9p23	0.0089289	0.0087624	chr9:1-12687261	53
17p13.1	0.011067	0.010406	chr17:8868260-9481705	2
4q34.3	0.00023669	0.023986	chr4:171810753-191154276	93
13q12.11	0.017488	0.053334	chr13:20795889-23727991	27
11p15.5	0.05384	0.05384	chr11:1-63334217	735
6q26	0.062808	0.065177	chr6:161693099-163153207	1
17q21.32	0.067872	0.067156	chr17:40085666-46187564	168
11q14.1	0.048815	0.095268	chr11:78125247-105481660	143
11q23.2	0.057245	0.11079	chr11:102666317-135006516	308
9q33.3	0.078599	0.11616	chr9:80906981-141213431	631
14q21.1	0.12401	0.12349	chr14:39652220-44977111	6
15q11.2	1.8813e-07	0.12349	chr15:1-65117646	421
Xq25	0.12349	0.12349	chrX:120183502-155270560	310
7q11.22	0.13331	0.13269	chr7:69000716-70601215	2
10q23.31	0.13269	0.13269	chr10:76581579-135534747	480
18q22.2	0.13784	0.13269	chr18:47089955-78077248	134
19q13.33	0.13587	0.13269	chr19:37145637-59128983	805
16p13.3	0.14626	0.14603	chr16:1-1834723	83
12q24.31	0.034824	0.1621	chr12:120875791-133851895	141
9q21.13	0.095127	0.1969	chr9:35101925-141213431	796
7q36.2	0.20205	0.20297	chr7:73701915-159138663	703

Genes in Wide Peak

This is the comprehensive list of deleted 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
FSTL3
POLR2E
ARID3A
CFD
MIR4745
RNA5SP462
OR4F17
FAM138F
WASH5P
AZU1
HCN2
BSG
CDC34
CNN2
ELANE
GPX4
GZMM
PALM
POLRMT
PRTN3
PTBP1
MADCAM1
PPAP2C
MED16
ABCA7
HMHA1
SHC2
FGF22
THEG
MIER2
RNF126
WDR18
LPPR3
KISS1R
R3HDM4
TMEM259
TPGS1
GRIN3B
MISP
C2CD4C
ODF3L2
PRSS57
MIR3187

Genes in Wide Peak

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

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

Genes
BUB1B
LINC00594
RNA5SP392
LINC00984
snoU13\|ENSG00000238564.1
THBS1
IVD
PLCB2
SRP14
GPR176
PAK6
DISP2
KNSTRN
BMF
FSIP1
C15orf52
C15orf54
EIF2AK4
C15orf56
PHGR1
ANKRD63

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q13.31.

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

Genes
LINC00901
TUSC7
RN7SL582P
MIR4447

Genes in Wide Peak

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

Table S28. 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 3p14.2.

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

Genes
FHIT
PBRM1
U3\|ENSG00000212211.1
NPCDR1
RPP14
RNU6ATAC26P
PDE12
snoU13\|ENSG00000238905.1
HESX1
RNA5SP133
RN7SKP45
MIR3938
ESRG
CHDH
SNORD63\|ENSG00000251987.1
SNORA26\|ENSG00000212608.1
SNORD38\|ENSG00000207109.1
RN7SL821P
snoU13\|ENSG00000238565.1
MUSTN1
SNORD69
SNORD19\|ENSG00000222345.1
SNORD19B\|ENSG00000238862.1
SNORD19\|ENSG00000212493.1
SNORD19B\|ENSG00000252787.1
RNU6ATAC16P
ARF4
CACNA1D
DNASE1L3
FLNB
ITIH1
ITIH3
ITIH4
PDHB
PRKCD
NEK4
TKT
WNT5A
SLMAP
ACOX2
RPP14
FAM107A
FAM208A
ERC2
APPL1
GNL3
SPCS1
ARHGEF3
SFMBT1
IL17RD
PXK
IL17RB
CACNA2D3
DCP1A
GLT8D1
ABHD6
LRTM1
SELK
RFT1
ACTR8
FAM3D
ASB14
C3orf67
KCTD6
DNAH12
DENND6A
CCDC66
SPATA12
TMEM110

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp21.1.

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

Genes
MIR3915
RNA5SP501

Genes in Wide Peak

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

Table S31. 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 12q23.1.

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

Genes
RNA5SP366
FAM71C

Genes in Wide Peak

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

Table S33. 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 4q22.1.

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

Genes
RN7SKP248
CCSER1

Genes in Wide Peak

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

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

Genes
RB1
RCBTB2
LPAR6

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.31.

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

Genes
ARSA
RN7SL500P
DENND6B
TTLL8
ALG12
RN7SKP252
CDPF1
C22orf26
LINC00899
MIR4762
MIR1249
LINC00229
SCUBE1
RNU12
RN7SKP80
RRP7B
RRP7A
snoU13\|ENSG00000238498.1
LINC00634
SHISA8
MIR33A
RNU6ATAC22P
ACR
BIK
TSPO
MPPED1
CHKB
CPT1B
CYP2D7P1
CYP2D6
CYB5R3
TYMP
FBLN1
XRCC6
NAGA
NDUFA6
NHP2L1
PMM1
PPARA
MAPK11
MAPK12
SBF1
SREBF2
TCF20
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
PACSIN2
GRAMD4
TTLL12
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
TBC1D22A
TTLL1
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
ARFGAP3
SMC1B
MCAT
DESI1
PARVB
NCAPH2
GTSE1
A4GALT
MOV10L1
FAM118A
TTC38
MIOX
PRR5
TRMU
SEPT3
PANX2
PARVG
CERK
EFCAB6
CENPM
CRELD2
C22orf46
CCDC134
ADM2
TRABD
PNPLA3
HDAC10
LDOC1L
POLDIP3
KIAA1644
SHANK3
TUBGCP6
LMF2
SMDT1
SERHL
PHF21B
KLHDC7B
TNFRSF13C
MEI1
FAM109B
NFAM1
PNPLA5
WBP2NL
SERHL2
ATP5L2
C22orf34
LINC00207
FLJ27365
LINC00898
IL17REL
MIRLET7A3
MIRLET7B
PIM3
ODF3B
ARHGAP8
SYCE3
MIR3201
MIR3619
MIR3667
MIR4763
MIR378I
MIR4535

Genes in Wide Peak

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

Table S37. 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 8p23.2.

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

Genes
PCM1
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
SNORA70\|ENSG00000206661.1
RN7SL872P
RNA5SP251
RPL23AP53
OR4F21
NAT1
NAT2
ADRA1A
ANGPT2
ASAH1
ATP6V1B2
BLK
BMP1
POLR3D
BNIP3L
CHRNA2
CLU
CTSB
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
DPYSL2
EGR3
DMTN
EPHX2
CLN8
EXTL3
PTK2B
FDFT1
FGL1
GATA4
GFRA2
GNRH1
LOXL2
LPL
MSR1
MSRA
NEFM
PDGFRL
PNOC
PPP2R2A
PPP3CC
SFTPC
SLC7A2
SLC18A1
STC1
FZD3
TUSC3
TNKS
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
DOK2
MYOM2
DLGAP2
MFHAS1
ENTPD4
ARHGEF10
PHYHIP
KBTBD11
SORBS3
NPM2
DLC1
SPAG11B
PNMA2
ADAM28
LZTS1
XPO7
TRIM35
RHOBTB2
KIF13B
PSD3
SLC39A14
FBXO25
ADAMDEC1
CNOT7
SCARA3
KCTD9
PINX1
PIWIL2
ELP3
INTS10
CCDC25
INTS9
CSGALNACT1
HR
PBK
ZNF395
BIN3
MTUS1
KIAA1456
KIAA1967
SH2D4A
PDLIM2
CSMD1
EBF2
FAM160B2
MTMR9
HMBOX1
MCPH1
PPP1R3B
DOCK5
REEP4
STMN4
SOX7
FAM167A
SLC35G5
FAM86B1
ERI1
LONRF1
CHMP7
RP1L1
CLDN23
VPS37A
SGCZ
DEFB104A
PEBP4
CDCA2
ESCO2
FBXO16
TDRP
ERICH1
TDH
C8orf48
ZNF596
R3HCC1
PRSS55
C8orf74
LGI3
DEFB106A
DEFB107A
DEFB130\|ENSG00000232948.1
NEIL2
XKR6
MICU3
SCARA5
USP17L2
NUGGC
LINC00599
MIR320A
DEFB103A
DEFB107B
DEFB104B
DEFB106B
C8orf58
DEFB135
DEFB136
SPAG11A
MIR596
DEFA1B
ZNF705D
ZNF705B
DEFB4B
MIR548I3
MIR548H4
MIR4288
MIR4286
MIR3622B
MIR4660
MIR5692A2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.21.

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
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
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
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 9p23.

Table S40. 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
RN7SL412P
FAM138C
DMRT1
FOXD4
GLDC
PTPRD
RFX3
RLN1
RLN2
SLC1A1
SMARCA2
VLDLR
KIAA0020
RCL1
DMRT2
INSL6
KDM4C
KANK1
RANBP6
SPATA6L
PLGRKT
CBWD1
KIAA1432
DMRT3
ERMP1
PDCD1LG2
DOCK8
TPD52L3
IL33
C9orf123
UHRF2
C9orf66
KIAA2026
KCNV2
GLIS3
PPAPDC2
MIR4665

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.1.

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

Genes
STX8
NTN1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q34.3.

Table S42. 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
AGA
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
GPM6A
HPGD
ING2
IRF2
KLKB1
MTNR1A
VEGFC
GLRA3
SORBS2
SAP30
HAND2
ADAM29
FAM149A
FBXO8
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 13q12.11.

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

Genes
RNY3P4
LINC00621
SNORD36\|ENSG00000253094.1
LINC00424
RN7SL766P
snoU13\|ENSG00000238878.1
ZDHHC20
RNA5SP25
MIPEPP3
ESRRAP2
RN7SL80P
SNORD27\|ENSG00000252128.1
snoU13\|ENSG00000238893.1
HNRNPA1P30
MIR4499
FGF9
IFT88
SAP18
GJB6
LATS2
CRYL1
IL17D
XPO4
MRP63
N6AMT2
SKA3
MICU2

Genes in Wide Peak

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

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

Genes
CARS
DDB2
EXT2
FANCF
HRAS
LMO1
LMO2
NUP98
WT1
CREB3L1
SLC22A10
RN7SL259P
SNHG1
RN7SL119P
TMEM223
C11orf83
SNORA57\|ENSG00000206597.1
METTL12
MIR3654
MIR1908
MIR611
RPLP0P2
SYT7
RN7SL23P
SDHAF2
PGA4
PGA3
MS4A18
MS4A4E
MS4A2
OOSP1
RN7SKP192
MIR3162
RN7SL435P
RN7SL42P
GLYATL1P2
BTBD18
C11orf31
RTN4RL2
RN7SKP259
RNA5SP341
PRG2
P2RX3
snoU13\|ENSG00000238692.1
OR5G5P
TRIM51HP
TRIM49B
OR4C5
MIR3161
RNA5SP340
snoU13\|ENSG00000252447.1
KBTBD4
PTPMT1
RN7SL652P
RN7SL772P
SNORD67\|ENSG00000212135.1
SNORD67\|ENSG00000252427.1
MIR5582
HARBI1
MIR4688
PHF21A
CHST1
CD82
C11orf96
RN7SKP287
HNRNPKP3
SNORA31\|ENSG00000251838.1
TRAF6
COMMD9
MIR3973
TRIM44
MIR1343
EHF
CD59
C11orf91
EIF3M
U3\|ENSG00000212551.1
DNAJC24
ARL14EP
RN7SL240P
RN7SKP158
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
ACP2
AP2A2
APLNR
AMPD3
APBB1
RHOG
ARHGAP1
ARNTL
ART1
ASCL2
BDNF
SERPING1
MPPED2
MYRF
TMEM258
DAGLA
CALCA
CALCB
CAT
CCKBR
CD5
CD6
MS4A1
MS4A3
CD44
CD81
CD151
CDKN1C
CHRM1
CHRM4
TPP1
CNGA4
CNTF
COPB1
CRY2
CSTF3
CTNND1
CTSD
DDB1
DRD4
DUSP8
EEF1G
EIF4G2
ELF5
F2
FEN1
FOLH1
FSHB
FTH1
GAS2
GIF
GNG3
GTF2H1
HBB
HBD
HBE1
HBG2
HPX
IGF2
ILK
INCENP
INS
IRF7
KCNA4
KCNC1
KCNJ11
KCNQ1
LDHA
LDHC
FADS1
FADS3
LRP4
LSP1\|ENSG00000130592.9
CAPRIN1
MDK
SCGB2A1
SCGB2A2
MUC2
MUC6
MYBPC3
MYOD1
NAP1L4
NDUFS3
NELL1
NUCB2
SLC22A18
OSBP
PAX6
PDE3B
PGA5
PIK3C2A
POLR2G
POLR2L
PSMA1
PSMC3
PSMD13
PTH
PTPRJ
RAB3IL1
RAG1
RAG2
RAPSN
RARRES3
RCN1
RNH1
ROM1
MRPL23
RPL27A
RPS13
RRM1
SAA1
SAA2
SAA4
SLC1A2
SLC3A2
SMPD1
SPI1
TRIM21
SSRP1
ST5
STIM1
STX3
STX5
ABCC8
TALDO1
TCN1
TEAD1
TH
TSPAN4
TNNI2
TNNT3
TSG101
PHLDA2
TUB
SCGB1A1
BEST1
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
CSRP3
PDHX
BBOX1
PPFIBP2
SLC43A1
IFITM1
DGKZ
API5
MADD
OR6A2
DCHS1
EIF3F
BRSK2
MTA2
UBE2L6
SLC22A6
SLC22A8
LPXN
PEX16
FADS2
MAPK8IP1
TP53I11
MICAL2
CTR9
ATG13
CKAP5
TRIM66
NR1H3
TSPAN32
TSSC4
USH1C
HIPK3
PRMT3
GLYAT
MRVI1
TRIM22
PRG3
IFITM3
NXF1
DEAF1
IPO7
HTATIP2
IFITM2
TRIM3
TAF6L
SCGB1D2
SCGB1D1
CELF1
OR5I1
CLP1
PKP3
HPS5
PTGDR2
RRAS2
ZP1
SWAP70
GANAB
DTX4
DENND5A
NUP160
FNBP4
SIRT3
OR52A1
ARFIP2
MTCH2
FJX1
KIAA1549L
ABTB2
PAMR1
ZDHHC5
DAK
B3GAT3
FBXO3
SERGEF
OR5L2
OR10A3
TIMM10B
TIMM10
BSCL2
ELP4
DKK3
RBMXL2
PGAP2
PRPF19
SLC43A3
PACSIN3
TRPM5
UBQLN3
RNF141
UBXN1
APIP
TMX2
HSD17B12
TMEM216
BET1L
CEND1
SLC15A3
MS4A4A
TMEM138
CYB5R2
CDHR5
TOLLIP
ZDHHC13
WDR74
MS4A12
MRPL16
TMEM132A
HRASLS2
USP47
VPS37C
TRIM68
NAT10
UEVLD
LIN7C
SLC35C1
TCP11L1
LGR4
PIDD
KCNQ1DN
SOX6
AMBRA1
KBTBD4
TTC17
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
PRDM11
CHRNA10
SLC17A6
PNPLA2
SYT13
PHRF1
LRRC4C
SCUBE2
MS4A7
ZBED5
SIGIRR
ALX4
RIC8A
MRPL17
FAM111A
ANO3
MS4A6A
MS4A5
EPS8L2
TUT1
STK33
CHID1
AHNAK
PRRG4
TMEM109
CCDC86
C11orf48
C11orf49
TRIM48
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
E2F8
SLC25A22
ZNF408
QSER1
AGBL2
ZBTB3
CPSF7
PRR5L
ASRGL1
ATHL1
INTS5
ZFP91
OR8J3
OR51G2
OR51E2
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
OR10W1
PTDSS2
SBF2
KIF18A
MS4A8
FAM160A2
FAR1
BTBD10
ARFGAP2
ACCS
MS4A14
TRIM51
PTPN5
MICALCL
LGALS12
TRIM5
TNKS1BP1
NAV2
SYT8
TSPAN18
CCDC34
SLC39A13
DEPDC7
GLYATL1
PRKCDBP
SAAL1
SLC22A9
OSBPL5
C1QTNF4
LRRC56
MRGPRE
ART5
MRGPRX2
MRGPRX3
MRGPRX4
HRASLS5
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
C11orf74
OR4C46
OR4X2
OR4B1
OR52M1
OR52K2
OR5P2
OR5P3
GYLTL1B
CYP2R1
DBX1
OR8I2
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
LDLRAD3
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
MUC15
C11orf94
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
SLC5A12
LDHAL6A
C11orf42
NLRP6
METTL15
IMMP1L
OR56B4
ANO5
OR8U1
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR5AS1
OR8K5
OR5T2
OR8H1
OR8K3
OR8J1
OR5R1
OR5M3
OR5M8
OR5M11
OR5AR1
LRRC55
SMTNL1
YPEL4
MED19
OR6Q1
OR9I1
OR9Q1
OR9Q2
OR1S2
OR1S1
OR10Q1
OR5B17
OR5B21
GLYATL2
MPEG1
OR5A2
OR5A1
OR4D6
OR4D11
PATL1
PLAC1L
MS4A15
VWCE
CYB561A3
PPP1R32
LRRN4CL
HNRNPUL2
ALKBH3
MS4A6E
OR52B2
OR4C3
OR4S1
C11orf35
EML3
OR51F1
MRGPRX1
OR10AG1
OR5J2
OR4C13
OR4C12
CSNK2A3
OR51V1
OR9G4
LINC00301
EFCAB4A
TTC9C
SLC22A24
IGSF22
OR10A4
OLFML1
NLRP10
NLRP14
ANO9
LUZP2
OR5F1
OR5AP2
B4GALNT4
OR52L1
OR2AG2
OR52B6
OTOG
DCDC1
MS4A10
OR10A2
OVCH2
PDDC1
GALNT18
NCR3LG1
FAM111B
TMEM179B
MRGPRG
SLC22A25
IFITM5
FAM99A
OR56B1
INSC
FIBIN
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR10A6
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
OR5AK2
OR5B2
OR5B12
OR5AN1
OR4D10
OR4D9
OR10V1
LRRC10B
LINC00610
FAM180B
OR51T1
OR51A4
OR51A2
IFITM10
OR4A47
SCGB1D4
MIR130A
MIR210
TMEM41B
OR5B3
CCDC73
MS4A13
TRIM64C
MIR610
MUC5B
MIR302E
MIR670
MIR3159
MIR4298
MIR4299
MTRNR2L8
CCDC179
MIR4686
MIR4487
MIR4694
MIR4687
MIR4488

Genes in Wide Peak

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

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

Genes
PARK2

Genes in Wide Peak

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

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

Genes
BRCA1
ETV4
MIR152
PNPO
KPNB1
MRPL45P2
ITGB3
snoU13\|ENSG00000252088.1
RN7SL270P
LRRC37A17P
RNU6ATAC3P
FAM215B
RN7SL199P
RN7SL656P
RN7SL739P
LRRC37A4P
RN7SL730P
RNA5SP443
MAP3K14
FAM187A
CCDC103
RN7SL405P
RN7SL819P
FZD2
RN7SL258P
GPATCH8
U3\|ENSG00000221496.1
RN7SL507P
U3\|ENSG00000221044.1
C17orf105
LINC00910
LINC00854
SNORA40\|ENSG00000212149.1
RNY4P2
G6PC
AOC4P
CNTD1
CCR10
HSD17B1
MIR5010
MIR548AT
ZNF385C
TTC25
AOC2
ARL4D
ATP6V0A1
FMNL1
CDC27
CNP
CRHR1
DHX8
DUSP3
EZH1
KAT2A
GFAP
GRN
HCRT
IFI35
ITGA2B
ITGB3
NBR1
MAPT
ADAM11
MEOX1
MPP2
MPP3
MYL4
NAGLU
NFE2L1
NMT1
NSF
PPY
PYY
RAB5C
RPL27
SLC4A1
SP2
STAT3
STAT5A
STAT5B
MLX
DNAJC7
TUBG1
UBTF
WNT3
WNT9B
RND2
CNTNAP1
AOC3
BECN1
EFTUD2
NPEPPS
GOSR2
TBKBP1
PLEKHM1
LRRC37A
HDAC5
GJC1
PSME3
NBR2
RAMP2
VAT1
HEXIM1
C1QL1
RUNDC3A
CBX1
KCNH4
FAM215A
TUBG2
NKIRAS2
COA3
PSMC3IP
TBX21
SOST
COPZ2
ARL17A
SLC25A39
HIGD1B
ATXN7L3
WNK4
C17orf53
TMUB2
DHX58
PRR15L
ACBD4
DCAKD
PLEKHH3
DBF4B
CDK5RAP3
SP6
COASY
AARSD1
VPS25
TMEM101
GHDC
LRRC46
SCRN2
G6PC3
ASB16
HSPB9
PLCD3
TMEM106A
OSBPL7
SPATA32
HEXIM2
LSM12
CCDC43
EFCAB13
MRPL10
CD300LG
KIF18B
RUNDC1
NAGS
FAM134C
SPPL2C
ARHGAP27
STH
KANSL1
FAM171A2
C17orf104
PTRF
LINC00671
RPRML
LRRC37A2
MIR2117
ARL17B
MIR5089
PTGES3L

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q14.1.

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

Genes
MAML2
BIRC3
PICALM
RNA5SP348
MMP12
WTAPP1
snoU13\|ENSG00000239154.1
snoU13\|ENSG00000252679.1
MIR3920
snoU13\|ENSG00000238388.1
RN7SKP115
RN7SL222P
RN7SKP53
RNA5SP347
RNA5SP346
RNA5SP345
SRSF8
SRSF8
MIR548L
VSTM5
RN7SL195P
snoU13\|ENSG00000238437.1
MED17
SNORA40\|ENSG00000210825.1
SNORA18\|ENSG00000207145.1
SNORD5\|ENSG00000239195.1
SNORA8\|ENSG00000207304.1
SNORA1\|ENSG00000206834.1
SNORD6
SNORA32\|ENSG00000206799.1
SNORA25\|ENSG00000207112.1
SCARNA9
RN7SL223P
SLC36A4
snoU13\|ENSG00000239086.1
DISC1FP1
CHORDC1
SNORD56\|ENSG00000207299.1
TRIM49D1
TRIM64B
TRIM77
FOLH1B
GRM5
TMEM135
RN7SL225P
snoU13\|ENSG00000238666.1
PCF11
SNORA70E
snoU13\|ENSG00000238995.1
SNORD112\|ENSG00000252592.1
BIRC2
CASP1
CASP4
CASP5
CTSC
DLG2
FUT4
MMP1
MMP3
MMP7
MMP8
MMP10
MMP13
MRE11A
MTNR1B
PGR
PRCP
TRPC6
TYR
FZD4
JRKL
EED
MTMR2
MMP20
CEP57
NAALAD2
YAP1
ME3
GPR83
PRSS23
ENDOD1
RAB38
PANX1
TENM4
RAB30
C11orf54
NOX4
C11orf73
CWC15
CNTN5
SYTL2
ANKRD49
KDM4D
TMEM126B
SMCO4
TRIM49
KIAA1377
CREBZF
CARD18
CCDC90B
CCDC81
MMP27
TAF1D
DYNC2H1
NARS2
CCDC82
PDGFD
TMEM133
TMEM126A
DCUN1D5
C11orf70
KIAA1731
CARD16
TMEM123
FAT3
FAM76B
SESN3
PIWIL4
ARHGAP42
AMOTL1
CCDC67
C11orf82
CCDC83
FAM181B
CCDC89
ANGPTL5
ANKRD42
HEPHL1
FOLR4
KDM4E
DDI1
CARD17
TRIM49C
MIR708
MIR1261
MIR1304
MIR4300
MIR1260B
MIR3166
CASP12
MIR4490
MIR4693
MIR5579

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q23.2.

Table S48. 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 9q33.3.

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

Genes
ABL1
FANCC
NOTCH1
OMD
RALGDS
SET
SYK
TAL2
TSC1
XPA
NR4A3
BRD3
NUP214
FNBP1
FAM157B
TUBBP5
MRPL41
snoU13\|ENSG00000272272.1
RNF224
TMEM210
MIR3621
snoU13\|ENSG00000238824.1
SNORD62
CLIC3
C9orf141
MIR4479
C9orf172
MIR4292
LCN10
LCN6
SNHG7
FAM69B
MIR126
U3\|ENSG00000252440.1
MIR4673
DNLZ
DKFZP434A062
MIR4669
RXRA
RNU6ATAC
LINC00094
FAM163B
SNORD36C
SNORD36A
SNORD36B
SNORD24
ABO
snoU13\|ENSG00000238657.1
CELP
GTF3C4
SNORA67\|ENSG00000212395.1
RN7SL328P
SNORD62B
SNORD62A
PRRC2B
SNORA31\|ENSG00000252582.1
snoU13\|ENSG00000238298.1
RN7SL665P
HMCN2
ASB6
LINC00963
RN7SL159P
C9orf106
snoU13\|ENSG00000239055.1
RN7SL560P
HMGA1P4
URM1
MIR4672
RNA5SP296
SNORA65
SNORD116\|ENSG00000252985.1
NRON
RN7SL30P
MIR181A2HG
RN7SL302P
MIR601
GPR21
SNORD90
RN7SL227P
RBM18
RN7SL187P
GGTA1P
RN7SL181P
RN7SKP125
RN7SKP128
SNORA70C
LINC00474
TNFSF8
ATP6V1G1
snoU13\|ENSG00000238530.1
MIR455
COL27A1
FKBP15
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
U3\|ENSG00000252299.1
U6\|ENSG00000271923.1
SPATA31C1
SNORA26\|ENSG00000212421.1
RN7SKP264
IDNK
SNORD112\|ENSG00000252256.1
snoU13\|ENSG00000238608.1
RN7SKP242
SPATA31D3
SPATA31D4
SPATA31D5P
SNORD95\|ENSG00000200969.1
RNA5SP287
TLE4
ABCA1
ABCA2
AK1
ALAD
ALDOB
AMBP
ASS1
AUH
BAAT
C5
C8G
CACNA1B
CCBL1
ENTPD2
CDK9
CEL
CKS2
COL5A1
COL15A1
SLC31A1
SLC31A2
CRAT
CTSL
CYLC2
DAPK1
DBC1
DBH
SARDH
DNM1
ECM2
TOR1A
LPAR1
S1PR3
MEGF9
ENDOG
ENG
STOM
FBP1
FKTN
FCN1
FCN2
FOXE1
FPGS
NR5A1
FUT7
GAS1
NR6A1
GLE1
GNG10
GOLGA1
GOLGA2
RAPGEF1
GRIN1
GSN
HNRNPK
HSD17B3
HSPA5
TNC
IARS
LCN1
LCN2
LMX1B
MUSK
NCBP1
NDUFA8
NFIL3
NINJ1
NTRK2
ROR2
ODF2
OGN
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PHF2
PPP2R4
PPP3R2
PPP6C
PSMB7
PSMD5
PTCH1
PTGDS
PTGS1
PTPN3
RAD23B
RGS3
RPL7A
RPL12
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TGFBR1
TLE1
TLR4
TMOD1
TRAF1
TRAF2
TTF1
TXN
VAV2
CORO2A
ZFP37
ZNF79
ZNF189
LHX3
GFI1B
IKBKAP
CDC14B
TMEFF1
SSNA1
EDF1
CTNNAL1
FBP2
DPM2
FUBP3
PRPF4
KLF4
GTF3C5
LHX2
MED27
PTGES
GABBR2
RALGPS1
ADAMTSL2
TRIM14
PPP1R26
SEC16A
TNFSF15
PTBP3
SH2D3C
RABEPK
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
SEMA4D
ANP32B
AGPAT2
SPTLC1
POMT1
SMC2
ZBTB6
NEK6
SDCCAG3
NOXA1
USP20
ACTL7A
GADD45G
SPIN1
SEC61B
SLC27A4
SLC35D2
CNTRL
WDR5
C9orf9
ADAMTS13
CACFD1
SLC2A6
AKAP2
RPL35
MAN1B1
DOLK
ZNF510
HABP4
PTGR1
TRIM32
SETX
ERP44
ZBTB43
FAM120A
PMPCA
ASTN2
AGTPBP1
BICD2
KIAA0368
EXOSC2
NCS1
TDRD7
SLC44A1
ANGPTL2
NUP188
CDK20
RABGAP1
TMEM245
CIZ1
DFNB31
NELFB
NIPSNAP3A
NSMF
GPSM1
GAPVD1
PHF19
FBXW2
OR1J4
OR2K2
GBGT1
LHX6
OR1L3
OR1L1
OR1J2
TRUB2
ST6GALNAC4
INVS
NDOR1
TOR1B
TOR2A
NTMT1
PHPT1
ANAPC2
PKN3
DPP7
PSAT1
UBQLN1
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
DEC1
MRPS2
COQ4
CERCAM
EGFL7
GOLM1
PRRX2
C9orf114
C9orf156
RAB14
C9orf78
POLE3
NANS
FBXW5
MRPL50
RC3H2
EPB41L4B
TBC1D13
NUTM2F
DIRAS2
ASPN
BSPRY
TOR4A
TEX10
EXD3
FAM206A
NOL8
TMEM38B
NIPSNAP3B
STRBP
TBC1D2
HEMGN
KIF27
RABL6
CDK5RAP2
BARX1
RNF20
LRRC8A
INPP5E
NPDC1
BARHL1
SH3GLB2
REXO4
DOLPP1
KCNT1
ZBTB26
DENND1A
GPR107
SLC46A2
ZNF462
PRDM12
NAA35
SLC28A3
SUSD1
IPPK
DDX31
FAM129B
WNK2
SECISBP2
C9orf16
MAPKAP1
ZCCHC6
GALNT12
EHMT1
SVEP1
RMI1
PTGES2
GKAP1
AKNA
ISCA1
ARPC5L
HDHD3
AIF1L
UCK1
ZNF484
FSD1L
GARNL3
HSDL2
C9orf64
C9orf89
HIATL2
NTNG2
HIATL1
PPAPDC3
ZDHHC12
FAM73B
C9orf3
FIBCD1
KIAA1984
TMEM141
C9orf37
FGD3
MVB12B
WDR34
SAPCD2
C9orf69
LRSAM1
UAP1L1
MRRF
ARRDC1
DPH7
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
ZMYND19
GRIN3A
RNF183
NACC2
C9orf116
LCN8
PTRH1
PIP5KL1
PTPDC1
ANKRD19P
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
SLC34A3
DAB2IP
CAMSAP1
C9orf62
NXNL2
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
RASEF
TTC16
FAM120AOS
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
C9orf96
OLFML2A
QSOX2
ZNF367
C9orf91
NAIF1
ANKS6
SUSD3
CDC26
PHYHD1
MORN5
OR1L4
TXNDC8
FRMD3
C9orf43
CRB2
SCAI
C9orf117
C9orf47
SPATA31E1
LCN12
C9orf142
TPRN
FAM78A
OR13C9
OR13D1
GPR144
QRFP
OR1J1
OR1B1
MURC
GLT6D1
ERCC6L2
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
SPATA31D1
C9orf153
IER5L
C9orf171
LCN15
LRRC26
TMEM8C
CTSL3P
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
C9orf170
C9orf152
SNX30
WDR38
LCNL1
C9orf139
FAM166A
SOHLH1
ZBTB34
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR147A
MIR181A2
MIR181B2
MIR199B
NUTM2G
C9orf173
NRARP
C9orf129
DNAJC25
MIR600HG
MIR602
RNF208
CARD9
MIR3074
MIR3154
MIR4291
MIR4290
MIR4289
CCDC180
MIR3689A
MIR3911
MIR3927
MIR3689B
MIR3689D1
MIR3689F
MIR3960
MIR4674
MIR4478
MIR3689C
MIR3689D2
MIR4670
MIR3689E
MIR548AW

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q21.1.

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

Genes
SNORA31\|ENSG00000251858.1
FBXO33
CTAGE5
FSCB
MIA2
LRFN5

Genes in Wide Peak

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

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

Genes
BUB1B
TCF12
MIR1272
RN7SL707P
RN7SL595P
SNORA48\|ENSG00000252774.1
USP3
CA12
MIR190A
RN7SL613P
RNA5SP397
RNA5SP396
snoU13\|ENSG00000238767.1
MIR2116
C15ORF31
U3\|ENSG00000200318.1
RN7SKP95
snoU13\|ENSG00000239100.1
MYZAP
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
U3\|ENSG00000212511.1
CSNK1A1P1
MIR3942
ANP32AP1
GJD2
SNORA18\|ENSG00000252425.1
SLC12A6
TMCO5B
SNORD77\|ENSG00000212415.1
snoU13\|ENSG00000238342.1
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
RN7SL536P
GOLGA8S
RN7SL106P
HERC2P2
RN7SL495P
WHAMMP3
RN7SL545P
GOLGA8DP
MIR1268A
OR4N4
snoU13\|ENSG00000238960.1
DKFZP547L112
RN7SL400P
CT60
NBEAP1
RN7SL759P
GOLGA6L6
snoU13\|ENSG00000239083.1
CHEK2P2
RN7SL584P
ACTC1
ADAM10
ANXA2
APBA2
AQP9
BNIP2
CAPN3
CHRM5
CKMT1B
CYP19A1
DUT
EPB42
FBN1
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
GTF2A2
HDC
ITPKA
IVD
LIPC
LTK
MAP1A
MEIS2
MFAP1
TRPM1
MYO1E
MYO5A
NDN
NEDD4
OAZ2
OCA2
PLCB2
PPIB
MAPK6
RAB27A
RAD51
RORA
RYR3
SCG5
SLC12A1
SNRPN
SNX1
SPINT1
SRP14
TJP1
TP53BP1
TPM1
TYRO3
UBE3A
MKRN3
EIF3J
SNAP23
ALDH1A2
HERC2
HERC1
USP8
CCNB2
SLC28A2
CCPG1
GCNT3
COPS2
TRIP4
TGM5
PIGB
PPIP5K1
AQR
SECISBP2L
KIAA0101
ARHGAP11A
LCMT2
BCL2L10
RASGRP1
GNB5
ARPP19
SLC27A2
GPR176
CHP1
OIP5
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
ZNF609
RTF1
CYFIP1
MGA
DMXL2
VPS39
FAM189A1
AP4E1
DAPK2
EID1
NPAP1
SERF2
TMEM87A
RPAP1
BLOC1S6
GREM1
FOXB1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
DUOX2
MYEF2
RPS27L
NDUFAF1
NUSAP1
EMC4
SPTBN5
CTDSPL2
KLF13
RAB8B
DUOX1
CSNK1G1
DLL4
INO80
FAM63B
RNF111
ZNF280D
TRPM7
VPS13C
PPP1R14D
MTMR10
ZNF770
HAUS2
RMDN3
DNAJC17
MNS1
NOP10
MYO5C
NDNL2
FAM214A
EMC7
PAK6
DTWD1
CASC5
AVEN
STARD9
VPS18
SQRDL
ZNF106
RFX7
SPATA5L1
CHAC1
NARG2
KATNBL1
SLTM
SNX22
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
POLR2M
NIPA2
APH1B
TLN2
FAM96A
C15orf48
C15orf41
SPPL2A
ZFYVE19
CGNL1
FRMD5
DISP2
CHRFAM7A
ARHGAP11B
DPH6
C15orf57
KNSTRN
BMF
SHF
DUOXA1
LDHAL6B
CHST14
CASC4
LACTB
TUBGCP5
TGM7
CATSPER2
LEO1
NIPA1
PLA2G4E
TRIM69
C15orf43
C2CD4A
FAM81A
C15orf65
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
DYX1C1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
FAM227B
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
LYSMD2
NUTM1
WDR72
SLC24A5
PRTG
GOLGA6L2
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8I
FBXL22
GLDN
FMN1
RBPMS2
USP50
TEX9
C15orf52
TNFAIP8L3
C2CD4B
GOLGA8EP
OR4M2
SHC4
CTXN2
C15orf53
C15orf54
DUOXA2
HERC2P9
GOLGA8B
EIF2AK4
UNC13C
MIR422A
CKMT1A
SERINC4
C15orf62
GOLGA8N
C15orf56
PHGR1
MIR147B
ANKRD63
JMJD7
PLA2G4B
POTEB2
MIR1282
MIR4508
MIR4510
MIR4716
MIR4713
MIR4712
GCOM1
POTEB

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq25.

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

Genes
ELF4
GPC3
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
RN7SL667P
snoU13\|ENSG00000239037.1
PNMA6B
PNMA6D
PNMA6A
RN7SL190P
CETN2
CSAG2
CSAG4
MAGEA2B
CSAG3
GABRQ
MIR452
MIR224
U3\|ENSG00000253009.1
LINC00894
LINC00893
RN7SKP267
CXorf51A
CXorf51B
RNA5SP517
SPANXN1
RN7SKP189
RN7SKP149
RN7SKP81
snoU13\|ENSG00000239188.1
RNA5SP516
SPANXD
SPANXA2
SPANXA1
RN7SL727P
MIR505
SNORA18\|ENSG00000252719.1
RNU6ATAC23P
snoU13\|ENSG00000238485.1
MIR504
RN7SKP31
RN7SL325P
SNORD61\|ENSG00000206979.1
MIR934
snoU13\|ENSG00000239080.1
RNA5SP515
LINC00086
LINC00633
LINC00087
SMIM10
LINC00629
GPC4
SNORA8\|ENSG00000207100.1
RNA5SP514
RN7SL191P
FAM45B
RNA5SP513
DCAF12L2
snoU13\|ENSG00000238626.1
SNORA40\|ENSG00000252693.1
snoU13\|ENSG00000239058.1
RN7SL29P
U3\|ENSG00000212321.1
ABCD1
XIAP
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
BRS3
CD40LG
CDR1
CLIC2
CNGA2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
F9
FGF13
FHL1
FLNA
FMR1
AFF2
G6PD
GABRA3
GABRE
GDI1
GRIA3
HCFC1
HMGB3
HPRT1
IDH3G
IDS
IGSF1
IL9R\|ENSG00000124334.12
IRAK1
L1CAM
SH2D1A
MAGEA1
MAGEA2
MAGEA3
MAGEA4
MAGEA6
MAGEA8
MAGEA9
MAGEA10
MAGEA11
MAGEA12
MCF2
MECP2
MPP1
MTM1
OCRL
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SMARCA1
SOX3
SSR4
VAMP7\|ENSG00000124333.10
TAZ
VBP1
XPNPEP2
ZIC3
ZNF75D
ZNF185
F8A1
UBL4A
TMEM187
SLC10A3
TKTL1
IKBKG
MTMR1
APLN
FAM127A
SLC25A14
FAM50A
AIFM1
TMEM257
GPR50
RAB33A
ARHGEF6
MAGEC1
MAMLD1
BCAP31
TENM1
SPRY3\|ENSG00000168939.6
SLC9A6
ENOX2
STAG2
PLAC1
UTP14A
ZNF275
TREX2
LDOC1
FAM127B
SRPK3
RBMX
HTATSF1
PNMA3
CTAG2
NSDHL
ZDHHC9
TFDP3
MAGEC2
VGLL1
RBMX2
MST4
SASH3
CXorf48
TMLHE
SAGE1
PLXNA3
HAUS7
ZNF280C
MBNL3
MOSPD1
THOC2
PDZD4
RAP2C
FAM3A
BCORL1
SPANXC
PRRG3
BRCC3
MAP7D3
GPR101
CD99L2
H2AFB3
USP26
PHF6
TMEM185A
SLITRK2
FATE1
HS6ST2
FRMD7
CXorf40A
FAM58A
MMGT1
PNMA5
RAB39B
SLITRK4
SPANXN3
MAGEC3
PASD1
DCAF12L1
GPR112
GAB3
PNCK
ZFP92
ACTRT1
GPR119
CSAG1
FMR1NB
ARHGAP36
FAM122B
FAM122C
DDX26B
ZNF449
VMA21
CTAG1A
ATP11C
LINC00632
OR13H1
CCDC160
CXorf66
UBE2NL
MIR106A
MIR19B2
MIR92A2
FAM127C
CT45A3
CT45A4
CT45A5
SPANXN4
H2AFB2
H2AFB1
SPANXN2
MIR503HG
CT45A6
CT45A1
CXorf40B
MIR450A1
MIR363
MIR20B
MIR18B
MIR450A2
MIR503
MIR513A1
MIR513A2
MIR506
MIR507
MIR508
MIR510
MIR514A1
MIR514A2
MIR514A3
MIR542
MAGEA9B
OPN1MW2
SPANXB1
CT45A2
MIR767
MIR450B
MIR890
MIR891B
MIR888
MIR892B
MIR891A
MIR892A
LINC00892
HSFX2
CXorf64
SMIM9
SPANXB2
CMC4
PNMA6C
MIR513C
MIR320D2
MIR718
MIR513B
MIR2114
MIR514B
MIR4330
MIR3672
HSFX1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q11.22.

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

Genes
RN7SL371P
AUTS2

Genes in Wide Peak

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

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

Genes
PTEN
BMPR1A
FGFR2
TLX1
NFKB2
SUFU
MIR3944
TUBGCP2
C10orf91
BNIP3
PPP2R2D
LINC00959
MIR4297
MGMT
NPS
SNORD60\|ENSG00000199321.1
RNA5SP328
MIR4296
METTL10
GPR26
MIR3941
RN7SKP167
RN7SL846P
TIAL1
MIR4681
RN7SL749P
FAM45A
SNORA19\|ENSG00000222588.1
SNORA19\|ENSG00000207468.1
U3\|ENSG00000251836.1
LINC00867
EMX2OS
PDZD8
ENO4
snoU13\|ENSG00000238577.1
RN7SL384P
VWA2
NHLRC2
SNORA17\|ENSG00000212589.1
MIR4295
GUCY2GP
MIR548E
RNA5SP327
RN7SKP288
RN7SL686P
snoU13\|ENSG00000239125.1
SMNDC1
RN7SL450P
U4\|ENSG00000272160.1
RN7SKP278
RNA5SP326
RNA5SP325
snoU13\|ENSG00000238620.1
ITPRIP
MIR609
MIR936
RN7SL524P
OBFC1
C10ORF32
SFXN2
RN7SL21P
SNORD112\|ENSG00000253068.1
FGF8
snoU13\|ENSG00000239091.1
SNORD112\|ENSG00000252844.1
LBX1
HUG1
KAZALD1
MIR608
HIF1AN
NDUFB8
LINC00263
BLOC1S2
SNORA12\|ENSG00000212464.1
ERLIN1
snoU13\|ENSG00000238472.1
COX15
ENTPD7
snoU13\|ENSG00000238588.1
HPSE2
MIR4685
MIR1287
GOLGA7B
LINC00866
PI4K2A
EXOSC1
RNA5SP324
ZNF518A
CYP2C19
RNY4P26
PIPSL
RNA5SP323
HHEX
RN7SL644P
SNORA25\|ENSG00000252993.1
LINC00502
RN7SKP143
LINC00865
MIR107
IFIT1
snoU13\|ENSG00000238991.1
ANKRD22
SNORD74\|ENSG00000200891.1
RN7SL78P
CFL1P1
LINC00864
LINC00863
RN7SL733P
AGAP11
U3\|ENSG00000252189.1
MIR346
RNA5SP322
RN7SKP238
RN7SKP84
LINC00858
RGR
LINC00857
PLAC9
MBL1P
NUTM2E
NUTM2B
SFTPA1
SNORA71\|ENSG00000201393.1
LINC00595
LINC00856
RN7SL284P
RNA5SP321
SNORA31\|ENSG00000252888.1
RN7SL518P
MIR606
ACADSB
ACTA2
ADAM8
ADD3
ADRA2A
ADRB1
ANXA11
FAS
ARL3
CASP7
ENTPD1
CHUK
ABCC2
COL17A1
CPN1
CTBP2
CYP2C8
CYP2C9
CYP2C18
CYP2E1
CYP17A1
CYP26A1
DMBT1
DNTT
DOCK1
DUSP5
ECHS1
EMX2
GFRA1
GLUD1
GOT1
PRLHR
GRK5
GRID1
HABP2
HELLS
HMX2
HPS1
HTR7
IDE
IFIT2
IFIT3
INPP5A
KCNMA1
KIF11
ABLIM1
LIPA
MAT1A
MKI67
MXI1
NDUFB8
NRAP
OAT
PAX2
PDE6C
PGAM1
PITX3
PNLIP
PNLIPRP1
PNLIPRP2
PPP1R3C
HTRA1
PSD
PTPRE
ALDH18A1
RBP4
RGS10
RPS24
SCD
SFRP5
SFTPD
FBXW4
SLC18A2
SLIT1
SNCG
TAF5
TCF7L2
TECTB
TLL2
UROS
VDAC2
WNT8B
XPNPEP1
SHOC2
ADAM12
UTF1
LIPF
EIF3A
GBF1
LDB1
BTRC
CH25H
PKD2L1
BTAF1
PAPSS2
INA
PDLIM1
SMC3
NEURL
BUB3
LGI1
NOLC1
DLG5
GSTO1
BAG3
MINPP1
KIF20B
SH3PXD2A
FAM53B
SLK
DCLRE1A
FRAT1
PPIF
ACTR1A
NPM3
GLRX3
RPP30
DPYSL4
TACC2
SORBS1
NRG3
MGEA5
PRDX3
ADIRF
VAX1
ATE1
POLR3A
LDB3
SEC23IP
RAB11FIP2
CPEB3
INPP5F
NT5C2
PDCD11
SORCS3
WAPAL
PPRC1
FAM175B
RRP12
TBC1D12
DNMBP
FRAT2
KAT6B
IFIT5
DPCD
SEC31B
ATRNL1
C10orf137
LRIT1
TCTN3
C10orf12
ANKRD2
CNNM1
MYOF
ANKRD1
GHITM
PDCD4
VENTX
R3HCC1L
POLL
BLNK
KCNIP2
CUZD1
CALY
CALHM2
CUTC
PLCE1
DUSP13
CHST15
ACSL5
PANK1
CCSER2
EXOC6
FAM35A
CCNJ
MARCH5
ZRANB1
TTC40
NSMCE4A
CNNM2
WBP1L
C10orf118
CRTAC1
CEP55
CWF19L1
RNLS
PI4K2A
WDR11
FAM178A
DHX32
TDRD1
BCCIP
C10orf2
TM9SF3
ZMIZ1
AS3MT
STAMBPL1
GPAM
KIAA1598
FAM160B1
SEMA4G
PLEKHA1
AVPI1
FAM204A
LHPP
MMS19
NOC3L
IKZF5
ZDHHC6
CUEDC2
FBXL15
C10orf76
HPS6
MMRN2
TMEM180
MCMBP
C10orf95
PLEKHS1
PDZD7
C10orf88
UBTD1
TMEM254
WDR96
LRRC27
TNKS2
TRIM8
TSPAN14
SFXN3
SLC25A28
ELOVL3
MARVELD1
C10orf11
PCGF6
LOXL4
ZDHHC16
FAM213A
DYDC2
PCGF5
GPR123
LZTS2
LCOR
MRPL43
AFAP1L2
PYROXD2
USMG5
ZNF503
ATAD1
ARHGAP19
KNDC1
MTG1
CDHR1
BBIP1
FANK1
OPALIN
SYCE1
OPN4
HOGA1
SORCS1
PRAP1
ZNF511
C10orf90
BTBD16
FAM24A
PSTK
PIK3AP1
MORN4
ZFYVE27
MMP21
COMTD1
FRA10AC1
C10orf32
GSTO2
SFR1
CALHM3
CLRN3
PNLIPRP3
SFXN4
CPXM2
C10orf129
SAMD8
LIPJ
TRUB1
VTI1A
DYDC1
EIF5AL1
HECTD2
FGFBP3
C10orf82
CACUL1
SLC35G1
CCDC147
PWWP2B
PPAPDC1A
PAOX
FAM24B
ZCCHC24
EBF3
CALHM1
CASC2
TCERG1L
HSPA12A
FUOM
JAKMIP3
STK32C
RBM20
FFAR4
KCNK18
DUPD1
LIPM
CYP26C1
NANOS1
LRIT2
HMX3
CCDC172
SH2D4B
C10orf99
SLC16A12
CC2D2B
ARMS2
TEX36
C10orf120
FOXI2
GOLGA7B
C10orf85
C10orf62
IFIT1B
FRG2B
SPRN
MIR146B
MIR202
FAM196A
FAM25A
LIPK
LIPN
MIR607
NUTM2A
NUTM2D
SFTPA2
TLX1NB
C10orf131
KLLN
MIR1307
MIR2110
MIR378C
MIR3157
MIR3663
MIR4680
MIR4682
MIR4484
LINC00601

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q22.2.

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

Genes
BCL2
MALT1
RBFA
RBFADN
SALL3
RNA5SP461
SNORA25\|ENSG00000199392.1
GALR1
LINC00683
ZNF516
SMIM21
ZADH2
RN7SL551P
RN7SL401P
MIR548AV
RNA5SP460
RN7SL795P
snoU13\|ENSG00000238988.1
RN7SL705P
RNF152
RN7SL342P
OACYLP
U8\|ENSG00000199713.1
RN7SL112P
SNORD28\|ENSG00000252284.1
FECH
U3\|ENSG00000212539.1
TXNL1
SNORA73\|ENSG00000201816.1
RNA5SP459
SNORA37
DCC
snoU13\|ENSG00000238885.1
RN7SL695P
ME2
RNA5SP458
RN7SL310P
RNA5SP457
SCARNA18\|ENSG00000252139.1
SCARNA17\|ENSG00000251992.1
SCARNA17\|ENSG00000267322.1
CDH7
CYB5A
KDSR
GRP
LMAN1
SMAD4
MBD1
MBP
MC4R
MYO5B
NARS
NFATC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
MAPK4
RAB27B
SERPINB3
SERPINB4
TCF4
ZNF236
SERPINB7
TNFRSF11A
MBD2
CTDP1
SOCS6
ONECUT2
VPS4B
TSHZ1
ACAA2
CD226
TXNL4A
POLI
ADNP2
PHLPP1
NEDD4L
WDR7
PIGN
RTTN
KCNG2
CDH20
CDH19
TIMM21
RAX
CXXC1
ST8SIA3
MEX3C
TMX3
ZCCHC2
ZNF532
ELAC1
ZNF407
CNDP2
KIAA1468
CCDC102B
PQLC1
CCDC68
NETO1
MRO
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
ALPK2
FAM69C
STARD6
CCBE1
CBLN2
C18orf54
FBXO15
SKA1
CCDC11
GTSCR1
DOK6
LINC00305
DYNAP
BOD1L2
LINC00908
HMSD
CPLX4
ATP9B
LINC00909
MIR122
HSBP1L1
C18orf63
MIR4529
MIR5011

Genes in Wide Peak

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

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

Genes
PPP2R1A
AKT2
BCL3
CD79A
ERCC2
KLK2
CIC
CBLC
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
APOC1P1
SNORA70\|ENSG00000253027.1
snoZ6\|ENSG00000252200.1
CEACAM22P
CEACAM20
ZNF180
ZNF234
RN7SL53P
ZNF284
ZNF223
RN7SL368P
ZNF576
ZNF575
CEACAMP10
PSG7
PSG10P
CXCL17
SNORD112\|ENSG00000252356.1
CEA
CEACAMP3
C19orf69
TGFB1
RN7SL34P
RN7SL718P
CYP2B7P1
CYP2G1P
NUMBL
RN7SL758P
SERTAD1
LGALS17A
EID2
RN7SL566P
IFNL4
snoU13\|ENSG00000251709.1
ACTN4
SPRED3
snoU13\|ENSG00000238838.1
RN7SL663P
ZNF790
A1BG
AP2A1
APOC1
APOC2
APOC4
APOE
KLK3
ATP1A3
AXL
BAX
BCAT2
BCKDHA
CEACAM1
BLVRB
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CEACAM5
CGB
CEACAM3
CEACAM7
CEACAM8
CEACAM4
CKM
AP2S1
CLC
CLPTM1
CRX
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2F1
DMPK
DMWD
ECH1
MEGF8
EMP3
ERCC1
ERF
FBL
ETFB
FCAR
FCGRT
FLT3LG
FOSB
FPR2
FPR3
FTL
FUT1
FUT2
GIPR
GPR4
GPR32
GRIK5
GRIN2D
ARHGAP35
GSK3A
GYS1
HAS1
FOXA3
HNRNPL
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KCNN4
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LGALS4
LGALS7
LHB
LIG1
LIM2
LIPE
BCAM
MAP3K10
MYBPC2
CEACAM6
NFKBIB
NKG7
CNOT3
NPAS1
NTF4
NUCB1
PAFAH1B3
PEG3
PLAUR
POLD1
POU2F2
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG9
PSG11
PSMC4
PSMD8
PTGIR
PTPRH
PVR
PVRL2
RELB
RPL18
RPL28
MRPS12
RPS5
RPS9
RPS11
RPS16
RPS19
RRAS
RTN2
RYR1
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPA
SNRPD2
SPIB
AURKC
SULT2B1
SULT2A1
SUPT5H
TNNI3
TNNT1
TULP2
NR1H2
VASP
XRCC1
ZFP36
ZNF8
ZNF17
ZNF28
MZF1
ZNF45
ZNF221
ZNF222
ZNF132
ZNF135
ZNF154
ZNF155
ZNF175
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZNF112
ZNF229
ZNF230
SYMPK
MIA
DPF1
LTBP4
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
FCGBP
UBE2M
ARHGEF1
DYRK1B
CYTH2
ZNF235
KCNK6
NCR1
NAPSA
GMFG
KLK4
ZNF432
DHX34
SAE1
TRIM28
ZNF256
LILRB2
PAK4
TOMM40
ZNF211
RABAC1
TRAPPC2P1
SPINT2
DLL3
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
HNRNPUL1
CLASRP
KPTN
MAP4K1
KLK8
PNKP
U2AF2
ATF5
ZFP30
PPP6R1
CARD8
SIRT2
SIPA1L3
ZC3H4
FBXO46
ETHE1
RPL13A
SYNGR4
LILRA4
ZIM2
NUP62
HSPBP1
PPP1R15A
PLD3
EML2
ZNF324
KLK5
ZNF345
PRKD2
ZNF473
CCDC9
PRPF31
IRF2BP1
FGF21
ZNF285
SIGLEC7
LYPD3
BBC3
DKKL1
SIGLEC9
SIGLEC8
C5AR2
CHMP2A
DHDH
ZNF544
EIF3K
UBE2S
SLC6A16
LGALS13
CYP2S1
STRN4
EPN1
SERTAD3
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF571
ZNF581
PTOV1
RAB4B
PAF1
PPP1R12C
TRPM4
ZNF586
QPCTL
FAM83E
EPS8L1
RASIP1
SARS2
TMEM160
PIH1D1
SAMD4B
ATP5SL
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
MED29
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
SMG9
IRGC
SPHK2
LGALS14
EXOSC5
MEIS3
CEACAM19
SLC17A7
NAT14
CD177
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
LRFN1
USP29
PLEKHA4
PRX
SPTBN4
MARK4
CATSPERG
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
DMRTC2
C19orf33
ELSPBP1
LIN7B
HIF3A
ZNF574
PLEKHG2
ZNF649
ZSCAN18
RPL23AP79
TSEN34
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
ZNF329
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
ADCK4
CNTD2
ZNF702P
ZNF606
ZNF614
FUZ
OPA3
ITPKC
B9D2
RSPH6A
ZNF611
MED25
TEX101
WDR87
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
ZNF527
CNFN
ZNF347
ZNF577
ZNF607
SUV420H2
C19orf48
ZBTB45
ZNF587
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
ZNF551
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
ZNF835
YIF1B
ZNF765
NLRP12
MYADM
ZNF845
ZNF585B
TIMM50
SHKBP1
CCDC114
ACPT
CGB5
CGB7
LENG9
CGB8
GNG8
PPP1R14A
EGLN2
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
FBXO17
KIR3DL3
RASGRP4
ZNF526
ZNF837
CLDND2
ZNF816
ZNF543
COX6B2
OSCAR
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZNF573
EID2B
IRGQ
ZNF428
RINL
FBXO27
C19orf47
ZFP28
VSIG10L
LINC00085
ZNF480
ZNF534
ZNF578
C19orf18
ZNF418
KLC3
IGSF23
LYPD4
TMEM190
HIPK4
TMC4
TPM3P9
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
ZNF420
NLRP4
ZNF542
ZNF582
ZNF583
FAM98C
CAPN12
LGALS16
TTC9B
CDC42EP5
ZNF569
ZNF570
ZNF836
ZNF610
ZNF320
ZNF497
ZNF550
ZNF296
DEDD2
ZNF579
ZNF114
ZNF567
ZNF383
ZNF781
ZNF780B
ZNF540
ZNF525
SPACA4
ZNF585A
NLRP7
GGN
CADM4
ZNF584
ZSCAN4
NLRP11
TMEM86B
PRR24
ZNF549
IL4I1
IFNL2
IFNL3
IFNL1
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
ZNF780A
C19orf54
PRR19
TMEM145
LYPD5
ZNF283
PPP1R37
NKPD1
TPRX1
MAMSTR
IZUMO1
EMC10
KLK9
SIGLECL1
ZNF615
ZNF841
VSTM1
TMEM150B
FAM71E2
HKR1
VN1R2
VN1R4
NLRP9
ZNF546
MYPOP
NANOS2
ZNF850
NCCRP1
SYCN
LEUTX
ZNF404
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
SELV
ZNF530
DNAAF3
ZNF233
LILRA5
ZNF829
ZNF568
B3GNT8
IGFL1
ZNF773
CEACAM16
BLOC1S3
IGFL3
ZNF808
ZNF470
ZNF749
ZNF324B
ZNF793
PAPL
PINLYP
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
PSG8
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
TMEM91
SBK2
LGALS7B
PHLDB3
MIR641
CCDC61
SHISA7
MIR769
SIGLEC14
SGK110
BSPH1
SRRM5
ZNF587B
MIR1323
MIR3191
MIR4323
PPP5D1
ZNF865
MIR4530
MIR4754
MIR4752

Genes in Wide Peak

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

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

Genes
MIR3177
CCDC154
PRSS29P
C1QTNF8
MSLNL
METRN
MIR3176
MIR5587
ITFG3
HBZ
SNRNP25
POLR3K
WASIR2
WASH4P
DDX11L10
ARHGDIG
CLCN7
HBA1
HBA2
HBM
HBQ1
MPG
NME3
NME4
CAPN15
SSTR5
TPSAB1
UBE2I
NPRL3
AXIN1
RGS11
CACNA1H
BAIAP3
RHBDL1
PIGQ
RAB11FIP3
IFT140
TELO2
MSLN
STUB1
MRPL28
MAPK8IP3
TPSD1
TPSG1
DECR2
SOX8
GNG13
LUC7L
CRAMP1L
RAB40C
TMEM8A
CHTF18
RHBDF1
NARFL
TPSB2
PDIA2
UNKL
LMF1
FAM173A
MRPS34
TMEM204
ITFG3
WDR24
HAGHL
C16orf13
FAM195A
GNPTG
RHOT2
HN1L
RPUSD1
TSR3
WFIKKN1
CCDC78
C16orf11
FBXL16
WDR90
EME2
NHLRC4
C16orf91
JMJD8
PRR25
PTX4
MIR662

Genes in Wide Peak

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

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

Genes
BCL7A
ANHX
ZNF891
ZNF140
RNU4ATAC12P
RNA5SP379
LRCOL1
MUC8
SNORA49
RNA5SP378
RNA5SP377
RNA5SP376
RAN
snoU13\|ENSG00000238822.1
RN7SL534P
snoU13\|ENSG00000238895.1
MIR3612
TMEM132C
LINC00508
LINC00507
LINC00944
LINC00943
LINC00939
TMEM132B
BRI3BP
RPL22P19
DNAH10OS
EIF2B1
SNORA9\|ENSG00000206897.1
SNRNP35
RNA5SP375
RN7SL133P
MIR4304
HCAR1
SNORA9\|ENSG00000252192.1
ZCCHC8
MLXIP
ORAI1
SNORA70\|ENSG00000201945.1
GATC
ACADS
SCARB1
COX6A1
STX2
GOLGA3
GTF2H3
HPD
MMP17
P2RX4
P2RX7
POLE
PSMD9
PXMP2
CLIP1
SFSWAP
HNF1A
UBC
ZNF10
ZNF26
ZNF84
CDK2AP1
ULK1
DENR
OASL
DYNLL1
SRSF9
HCAR3
HIP1R
PIWIL1
CABP1
NCOR2
KNTC1
MLEC
RNF10
MPHOSPH9
CAMKK2
ZNF268
TMED2
FZD10
P2RX2
SETD1B
ANKLE2
ABCB9
RIMBP2
ATP6V0A2
GALNT9
ARL6IP4
POP5
ANAPC5
TRIAP1
RHOF
SBNO1
CHFR
DIABLO
PITPNM2
EP400
DHX37
FBRSL1
DDX55
C12orf43
VPS33A
RSRC2
AACS
NOC4L
B3GNT4
OGFOD2
VPS37B
TCTN2
RNF34
CCDC92
PUS1
COQ5
CCDC62
KDM2B
UNC119B
C12orf65
TMEM132D
SLC15A4
SPPL3
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
PGAM5
RILPL2
DNAH10
LRRC43
GPR133
MORN3
DDX51
HCAR2
EP400NL
RILPL1
IL31
SETD8
ZNF605
MIR3908
MIR4419B
MIR4700
MIR5188

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q21.13.

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

Genes
GNAQ
ABL1
FANCC
NOTCH1
OMD
PAX5
RALGDS
SET
SYK
TAL2
TSC1
XPA
NR4A3
BRD3
NUP214
FNBP1
FAM157B
TUBBP5
MRPL41
snoU13\|ENSG00000272272.1
RNF224
TMEM210
MIR3621
snoU13\|ENSG00000238824.1
SNORD62
CLIC3
C9orf141
MIR4479
C9orf172
MIR4292
LCN10
LCN6
SNHG7
FAM69B
MIR126
U3\|ENSG00000252440.1
MIR4673
DNLZ
DKFZP434A062
MIR4669
RXRA
RNU6ATAC
LINC00094
FAM163B
SNORD36C
SNORD36A
SNORD36B
SNORD24
ABO
snoU13\|ENSG00000238657.1
CELP
GTF3C4
SNORA67\|ENSG00000212395.1
RN7SL328P
SNORD62B
SNORD62A
PRRC2B
SNORA31\|ENSG00000252582.1
snoU13\|ENSG00000238298.1
RN7SL665P
HMCN2
ASB6
LINC00963
RN7SL159P
C9orf106
snoU13\|ENSG00000239055.1
RN7SL560P
HMGA1P4
URM1
MIR4672
RNA5SP296
SNORA65
SNORD116\|ENSG00000252985.1
NRON
RN7SL30P
MIR181A2HG
RN7SL302P
MIR601
GPR21
SNORD90
RN7SL227P
RBM18
RN7SL187P
GGTA1P
RN7SL181P
RN7SKP125
RN7SKP128
SNORA70C
LINC00474
TNFSF8
ATP6V1G1
snoU13\|ENSG00000238530.1
MIR455
COL27A1
FKBP15
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
U3\|ENSG00000252299.1
U6\|ENSG00000271923.1
SPATA31C1
SNORA26\|ENSG00000212421.1
RN7SKP264
IDNK
SNORD112\|ENSG00000252256.1
snoU13\|ENSG00000238608.1
RN7SKP242
SPATA31D3
SPATA31D4
SPATA31D5P
SNORD95\|ENSG00000200969.1
RNA5SP287
TLE4
RN7SKP59
PCA3
snoU13\|ENSG00000238598.1
RNY4P1
RN7SKP47
RNA5SP286
snoU13\|ENSG00000238402.1
RNA5SP285
MIR204
RN7SL570P
CBWD3
PGM5P2
RNA5SP284
SNORA70\|ENSG00000252878.1
RN7SL787P
RNA5SP283
RN7SL544P
SNORA70\|ENSG00000252133.1
FAM27E1
RN7SL722P
SNORA70\|ENSG00000252617.1
FAM27E2
RN7SL565P
RN7SL343P
FAM95B1
SNORA70\|ENSG00000252724.1
RN7SL763P
FAM74A6
FAM74A2
RN7SL422P
FAM74A1
RN7SL462P
FAM74A5
RN7SL640P
FAM201A
SNX18P3
IGFBPL1
snoU13\|ENSG00000238313.1
U8\|ENSG00000200026.1
SHB
RN7SKP171
RN7SL463P
MIR4476
MIR4540
LINC00961
RGP1
RN7SL22P
RMRP
MIR4667
ABCA1
ABCA2
AK1
ALAD
ALDH1A1
ALDH1B1
ALDOB
AMBP
ANXA1
APBA1
ASS1
AUH
BAAT
KLF9
C5
C8G
CA9
CACNA1B
CCIN
CCBL1
ENTPD2
CD72
CDK9
CEL
CKS2
CLTA
COL5A1
COL15A1
SLC31A1
SLC31A2
CRAT
CTSL
CYLC2
DAPK1
DBC1
DBH
SARDH
DNM1
ECM2
TOR1A
LPAR1
S1PR3
MEGF9
ENDOG
ENG
STOM
FBP1
FKTN
FCN1
FCN2
FOXE1
FPGS
FXN
NR5A1
FUT7
GAS1
NR6A1
GCNT1
GLE1
GNG10
GOLGA1
GOLGA2
RAPGEF1
GRIN1
GSN
HNRNPK
HSD17B3
HSPA5
TNC
IARS
LCN1
LCN2
LMX1B
MUSK
NCBP1
NDUFA8
NFIL3
NINJ1
NPR2
NTRK2
ROR2
ODF2
OGN
ORM1
ORM2
PAEP
PAPPA
PDCL
PBX3
PCSK5
PGM5
PHF2
PPP2R4
PPP3R2
PPP6C
PRKACG
PSMB7
PSMD5
PTCH1
PTGDS
PTGS1
PTPN3
RAD23B
RGS3
RORB
RPL7A
RPL12
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TESK1
TGFBR1
TLE1
TLN1
TLR4
TMOD1
TPM2
TRAF1
TRAF2
TTF1
TXN
VAV2
CORO2A
ZFP37
ZNF79
ZNF189
ZFAND5
LHX3
GFI1B
PIP5K1B
RECK
IKBKAP
CDC14B
TMEFF1
SSNA1
EDF1
CTNNAL1
FBP2
DPM2
FUBP3
PRPF4
KLF4
GTF3C5
LHX2
GRHPR
FAM189A2
TJP2
MED27
PTGES
GABBR2
GDA
GNA14
RALGPS1
ADAMTSL2
TRIM14
MELK
RUSC2
PPP1R26
SEC16A
ZBTB5
TNFSF15
PTBP3
GNE
SH2D3C
RABEPK
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
CREB3
UNC13B
SEMA4D
ANP32B
AGPAT2
SPTLC1
POMT1
SMC2
ZBTB6
NEK6
SDCCAG3
NOXA1
USP20
ACTL7A
GADD45G
SPIN1
SEC61B
SLC27A4
SLC35D2
CNTRL
WDR5
C9orf9
ADAMTS13
CACFD1
SLC2A6
AKAP2
RPL35
MAN1B1
FRMPD1
DOLK
ZNF510
HABP4
PTGR1
TRIM32
SETX
ERP44
ZBTB43
SMC5
FAM120A
PMPCA
VPS13A
ASTN2
AGTPBP1
BICD2
KIAA0368
EXOSC2
NCS1
TDRD7
SLC44A1
ANGPTL2
NUP188
CDK20
RABGAP1
TMEM2
TMEM245
CIZ1
DFNB31
NELFB
NIPSNAP3A
NSMF
GPSM1
GAPVD1
PHF19
ZNF658
SPATA31A7
FBXW2
SPAG8
OR1J4
OR2K2
FBXO10
GBGT1
LHX6
OSTF1
OR1L3
OR1L1
OR1J2
TRUB2
ST6GALNAC4
INVS
NDOR1
SIT1
TOR1B
TOR2A
NTMT1
PHPT1
ANAPC2
PKN3
DPP7
PSAT1
UBQLN1
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
DEC1
EXOSC3
ABHD17B
MRPS2
COQ4
CERCAM
EGFL7
GOLM1
PRRX2
C9orf114
C9orf156
RAB14
TMEM8B
C9orf78
POLE3
NANS
FBXW5
MRPL50
RC3H2
EPB41L4B
TBC1D13
NUTM2F
DIRAS2
ASPN
BSPRY
TOR4A
TEX10
EXD3
FAM206A
NMRK1
NOL8
C9orf40
TMEM38B
RFK
NIPSNAP3B
STRBP
TBC1D2
HEMGN
KIF27
RABL6
CDK5RAP2
BARX1
RNF20
LRRC8A
INPP5E
NPDC1
OR2S2
BARHL1
SH3GLB2
REXO4
DOLPP1
KCNT1
ZBTB26
GBA2
DENND1A
GPR107
SLC46A2
ZNF462
PRDM12
NAA35
SLC28A3
SUSD1
POLR1E
IPPK
DDX31
FAM129B
WNK2
SECISBP2
C9orf16
MAPKAP1
DCAF10
ZCCHC6
GALNT12
EHMT1
CNTNAP3
SVEP1
RMI1
TRPM3
PTGES2
FAM214B
GKAP1
AKNA
ISCA1
ARPC5L
HDHD3
AIF1L
UCK1
ZNF484
FSD1L
CEP78
ZCCHC7
ANKRD20A1
GARNL3
HSDL2
C9orf64
C9orf89
HIATL2
NTNG2
HIATL1
HINT2
PPAPDC3
ZDHHC12
FAM73B
ARHGEF39
C9orf3
FIBCD1
KIAA1984
TMEM141
C9orf37
FGD3
MVB12B
WDR34
SAPCD2
C9orf69
LRSAM1
UAP1L1
SLC25A51
MRRF
ARRDC1
DPH7
TMEM203
KIF12
PALM2
SLC25A25
WDR31
ZNF618
FAM122A
ZMYND19
GRIN3A
TMC1
RNF183
NACC2
C9orf116
C9orf41
C9orf57
C9orf85
C9orf135
LCN8
PTRH1
PIP5KL1
PTPDC1
ANKRD19P
OR13C5
OR13C8
OR13C3
OR13C4
OR13F1
OR1L8
OR1N2
OR1N1
TRPM6
SLC34A3
RNF38
GLIPR2
DAB2IP
CAMSAP1
C9orf62
NXNL2
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
RASEF
TRMT10B
TTC16
FAM120AOS
ATP8B5P
ZNF483
C9orf84
KIAA1958
TSTD2
ZNF782
PRUNE2
C9orf96
OLFML2A
TMEM252
QSOX2
ZNF367
C9orf91
NAIF1
CCDC107
ANKS6
SUSD3
CBWD5
CDC26
ANKRD18A
PHYHD1
MORN5
OR1L4
TXNDC8
MAMDC2
FRMD3
C9orf43
CRB2
SCAI
C9orf117
C9orf47
SPATA31E1
LCN12
C9orf142
TPRN
FAM78A
OR13C9
OR13D1
FOXD4L3
GPR144
QRFP
OR1J1
OR1B1
MURC
FOXD4L4
GLT6D1
PTAR1
ERCC6L2
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
SPATA31A6
SPATA31D1
C9orf153
IER5L
C9orf171
LCN15
LRRC26
TMEM8C
FAM221B
OR13J1
CTSL3P
OR13C2
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
TOMM5
FAM74A4
C9orf170
C9orf152
SNX30
WDR38
LCNL1
C9orf139
FAM166A
SOHLH1
ZBTB34
MIRLET7A1
MIRLET7D
MIRLET7F1
MIR147A
MIR181A2
MIR181B2
MIR199B
ANKRD20A3
ANKRD20A2
NUTM2G
C9orf173
NRARP
FOXB2
C9orf129
FAM27A
DNAJC25
SPATA31A2
SPATA31A4
CBWD6
HRCT1
SPATA31A1
FOXD4L6
FOXD4L5
MSMP
MIR600HG
MIR602
FAM27D1
RNF208
SPATA31A3
SPATA31A5
CBWD7
CARD9
FAM74A3
CNTNAP3B
ANKRD20A4
FAM166B
FOXD4L2
FAM27E3
FAM27C
FAM27B
MIR1299
MIR3074
MIR3154
MIR4291
MIR4290
MIR4289
CCDC180
MIR3689A
MIR3911
MIR3927
MIR3689B
MIR3689D1
MIR4477A
MIR3689F
MIR3960
MIR4475
MIR4674
MIR4478
MIR3689C
MIR3689D2
MIR4670
MIR3689E
MIR548AW

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q36.2.

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

Genes
BRAF
CDK6
EZH2
HIP1
MET
SMO
AKAP9
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
RNA5SP241
RNA5SP240
U1\|ENSG00000271739.1
NAA38
RNA5SP239
CAPZA2
snoZ185
SNORA25\|ENSG00000202377.1
MIR3666
RNA5SP238
TSRM
TMEM168
IFRD1
RN7SKP187
RNA5SP237
snoU13\|ENSG00000238922.1
FLJ00325
U3\|ENSG00000238297.1
snoU109\|ENSG00000238832.1
RNA5SP236
SNORD112\|ENSG00000251911.1
RN7SL8P
LHFPL3
RN7SKP86
RN7SKP198
FAM185A
POLR2J2
MIR4467
MIR5090
MIR4285
SH2B2
SNORA48\|ENSG00000252824.1
RABL5
MIR4653
RN7SKP54
MUC3A
MUC3A
RN7SL549P
RN7SL750P
SAP25
RN7SL416P
RN7SL161P
STAG3L5P
PILRB
GATS
MIR4658
MIR106B
MIR93
MIR25
AZGP1P1
SNORA40\|ENSG00000222966.1
CYP3A4
snoU13\|ENSG00000239133.1
MYH16
snoU13\|ENSG00000238459.1
MIR3609
RN7SL13P
RN7SL478P
RN7SKP104
RN7SL252P
SHFM1
MIR591
PON1
snoU13\|ENSG00000238384.1
RN7SKP129
GNG11
MIR489
MIR653
RN7SL7P
GATAD1
snoU13\|ENSG00000238739.1
DPY19L2P4
SNORA67\|ENSG00000207094.1
snoU13\|ENSG00000238587.1
LINC00972
SEMA3A
RNA5SP235
MIR1255B1
RN7SL35P
RN7SL869P
RNA5SP234
RSBN1L
snoU13\|ENSG00000238453.1
RN7SL212P
snoU13\|ENSG00000238935.1
TMEM120A
SNORA14A
CCL24
RN7SL642P
NSUN5P1
STAG3L1
GATSL2
GATSL1
STAG3L2
RNA5SP233
AOC1
ACHE
AKR1B1
ARF5
ASNS
AZGP1
OPN1SW
BPGM
CACNA2D1
CALCR
CALD1
CASP2
CAV1
CAV2
KRIT1
CD36
CFTR
CHRM2
AP1S1
CLCN1
COL1A2
CPA1
CPA2
CUX1
CYP3A7
CYP3A5
CYP51A1
DLD
DLX5
DLX6
DYNC1I1
DPP6
SLC26A3
EN2
EPHA1
EPHB4
EPHB6
EPO
FLNC
GBX1
GNAI1
GNB2
GNGT1
GPR22
GRM3
GRM8
GTF2I
HGF
MNX1
AGFG2
HSPB1
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LAMB1
LEP
LRCH4
MCM7
DNAJB9
MDH2
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NPTX2
NRCAM
NRF1
OCM2
ORC5
SERPINE1
PAX4
PCOLCE
PDK4
SLC26A4
PEX1
CDK14
ABCB1
ABCB4
PIK3CG
PIP
PMS2P3
PODXL
POLR2J
PON2
PON3
POR
PPP1R3A
PRKAR2B
PRSS1
RELN
PSMC2
TAS2R38
PTN
PTPN12
PTPRN2
PTPRZ1
RARRES2
RHEB
SLC4A2
SLC13A1
SMARCD3
SPAM1
SRI
AKR1D1
SRPK2
SSBP1
SYPL1
TAC1
TAF6
TBXAS1
TFR2
TRIP6
UBE2H
VGF
VIPR2
ZAN
CLIP2
WNT2
XRCC2
YWHAG
ZNF3
ZKSCAN1
ZSCAN21
ZP3
ZYX
MTERF
TFPI2
ST7
ARHGEF5
ZNF212
TRRAP
FZD1
ZNF282
CUL1
TRIM24
BUD31
SGCE
MGAM
WASL
PLOD3
CLDN12
DGKI
AP4M1
ATP6V1F
ASIC3
PMPCB
ATP5J2
GTF2IRD1
PDIA4
UBE3C
FAM131B
SEMA3E
DOCK4
FAM115A
MAGI2
DMTF1
DNAJB6
ABCF2
MUC12
ARPC1B
NAMPT
RASA4
SLC25A13
LRRC17
POP7
BET1
CCL26
FAM3C
COG5
ZNHIT1
SEMA3C
ARPC1A
STAG3
FGL2
CPSF4
FASTK
DBF4
COPS6
DUS4L
ZNF277
ABCB8
TP53TG1
PDAP1
TFEC
LAMB4
LMTK2
POMZP3
PAXIP1
KLHDC10
PEG10
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
ZKSCAN5
CLDN15
BRI3
TECPR1
POT1
PTCD1
CNTNAP2
TES
GIMAP2
OR2F1
FBXO24
SLC13A4
STEAP1
HBP1
DNAJC2
TPK1
SND1
DENND2A
ZNF777
PCLO
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
MDFIC
PILRA
FSCN3
ATP6V0A4
PNPLA8
TAS2R3
TAS2R4
TAS2R16
FIS1
CPA4
WNT16
ACTL6B
PRKAG2
ZC3HC1
SRRT
MRPS33
STYXL1
ASB4
NUB1
ADAM22
GSAP
GPR85
TAS2R5
ANKIB1
CHPF2
PUS7
ING3
LRRN3
CROT
ALKBH4
SAMD9
NCAPG2
CHCHD3
ZCWPW1
WDR60
RBM28
C7orf43
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
PPP1R9A
CCDC132
METTL2B
KMT2E
BAIAP2L1
SLC25A40
BCAP29
MEPCE
TRPV5
ANKRD7
ZC3HAV1
SLC12A9
ACN9
AKR1B10
SMURF1
PHTF2
ACTR3B
KIAA1147
RHBDD2
STRIP2
ESYT2
ZNF398
CCDC146
KMT2C
EXOC4
RINT1
GALNT11
LRRC4
LMBR1
NOM1
MOSPD3
GIGYF1
CCDC136
PARP12
CYP3A43
CASD1
LRRC61
C7orf49
ZNF655
PVRIG
TMEM243
GCC1
STEAP4
GAL3ST4
PRKRIP1
C7orf63
CBLL1
ZNF767
CPED1
TTC26
ORAI2
UPK3B
JHDM1D
OR2AE1
WBSCR16
TSC22D4
TRIM56
TMUB1
ARMC10
IMMP2L
CTTNBP2
RBM48
ZNF394
GTF2IRD2
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
TMEM60
GTPBP10
TRIM4
ADCK2
PLXNA4
ZC3HAV1L
MYL10
CADPS2
CPA5
FOXP2
CEP41
ZBED6CL
DTX2
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
COL26A1
PRSS37
KLF14
SSMEM1
SVOPL
MTPN
LRGUK
ASB10
PRSS58
SRCRB4D
ASZ1
MUC17
RNF32
ASB15
RUNDC3B
C7orf60
CLEC2L
C7orf55
IQUB
C7orf66
TMEM213
GIMAP8
CRYGN
ZNF425
ZNF746
ATP6V0E2
RBM33
GALNTL5
RNF133
THAP5
CCDC71L
GIMAP7
ZNF467
BHLHA15
ZNF800
GIMAP1
C7orf33
SAMD9L
C7orf62
ZNF804B
ZSCAN25
FAM200A
PPP1R35
GPC2
SRRM3
KIAA1324L
LRWD1
FBXL13
NAPEPLD
ATXN7L1
CDHR3
TMEM130
NYAP1
SEMA3D
CNPY4
POLR2J2
HEPACAM2
UBN2
MBLAC1
FAM133B
TAS2R39
TAS2R40
TAS2R41
STEAP2
CNPY1
FAM115C
ZNF775
ATG9B
ZNF789
LSMEM1
TAS2R60
BLACE
CTAGE6
AGBL3
OR6V1
OR2A12
OR2A1
GNAT3
MOGAT3
FAM71F2
STRA8
WDR86
GJC3
DPY19L2P2
GATS
GSTK1
TRIM73
NAT16
SLC26A5
RNF148
GTF2IRD2B
LAMTOR4
FEZF1
FAM180A
OR2A25
OR2A5
RPL13AP17
LRRD1
C7orf76
PRRT4
RAB19
OR2A7
OR2A42
KPNA7
C7orf61
UFSP1
MIR182
MIR183
MIR96
SPDYE3
SPDYE2
AKR1B15
CTAGE15
OR2A2
LMOD2
ARHGEF35
GIMAP6
WEE2
POLR2J3
MIR490
ZNF862
NCF1
ACTR3C
TMEM229A
POM121C
CTAGE4
EFCAB10
UPK3BL
CTAGE8
RASA4B
SMKR1
ZNF783
SPDYE2B
MIR548O
MIR548F4
MTRNR2L6
TMEM178B
MIR4652
MIR4468
MIR4651
MIR5692C2
MIR5707
MIR5692A1

Arm-level results

Table 3. Get Full Table Arm-level significance table - 21 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	0.51	2.14	0.124	0.28	-0.939	1
1q	1195	0.65	3.9	0.000977	0.38	0.114	0.81
2p	624	0.43	-0.263	1	0.06	-4.43	1
2q	967	0.39	-0.192	1	0.06	-4.16	1
3p	644	0.29	-1.73	1	0.48	0.505	0.599
3q	733	0.54	1.37	0.348	0.44	0.127	0.81
4p	289	0.33	-1.48	1	0.67	2.52	0.0266
4q	670	0.09	-3.28	1	0.63	2.84	0.0117
5p	183	0.44	-0.732	1	0.35	-1.78	1
5q	905	0.19	-2.72	1	0.39	-0.307	0.877
6p	710	0.58	2.1	0.124	0.22	-2.21	1
6q	556	0.55	1.39	0.348	0.24	-2.28	1
7p	389	0.45	-0.285	1	0.42	-0.635	0.975
7q	783	0.40	-0.383	1	0.33	-1.15	1
8p	338	0.53	0.599	0.812	0.65	2.17	0.0515
8q	551	0.60	1.86	0.186	0.45	-0.0115	0.82
9p	301	0.20	-2.53	1	0.69	3.02	0.00873
9q	700	0.06	-3	1	0.73	4.38	0.000241
10p	253	0.60	1.21	0.418	0.68	2.41	0.0331
10q	738	0.49	0.669	0.812	0.54	1.37	0.249
11p	509	0.14	-3.46	1	0.52	0.889	0.426
11q	975	0.22	-2.1	1	0.49	1.27	0.269
12p	339	0.49	0.118	1	0.42	-0.744	0.989
12q	904	0.26	-1.94	1	0.31	-1.34	1
13q	560	0.50	0.533	0.812	0.63	2.35	0.035
14q	938	0.24	-1.8	1	0.55	2.08	0.0594
15q	810	0.17	-2.52	1	0.62	2.84	0.0117
16p	559	0.39	-0.582	1	0.70	3.45	0.00287
16q	455	0.32	-1.3	1	0.74	3.91	0.000637
17p	415	0.24	-1.93	1	0.75	4.06	0.000512
17q	972	0.45	0.582	0.812	0.46	0.77	0.468
18p	104	0.46	-0.583	1	0.49	-0.252	0.877
18q	275	0.39	-1.17	1	0.48	-0.133	0.839
19p	681	0.56	1.6	0.279	0.50	0.744	0.468
19q	935	0.62	2.83	0.0242	0.52	1.25	0.269
20p	234	0.76	3.69	0.00152	0.37	-1.07	1
20q	448	0.84	5.21	3.8e-06	0.47	0.011	0.82
21q	258	0.46	-0.337	1	0.45	-0.507	0.949
22q	564	0.35	-0.995	1	0.69	3.29	0.00408
Xp	418	0.36	-1.3	1	0.47	-0.0501	0.82
Xq	668	0.28	-1.79	1	0.51	0.999	0.383

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/UCS-TP/19080987/GDAC_MergeDataFiles_12187647/UCS-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 56 Input Tumor Samples.

Tumor Sample Names
TCGA-N5-A4RA-01A-11D-A28Q-01
TCGA-N5-A4RD-01A-11D-A28Q-01
TCGA-N5-A4RF-01A-11D-A28Q-01
TCGA-N5-A4RJ-01A-11D-A28Q-01
TCGA-N5-A4RM-01A-11D-A28Q-01
TCGA-N5-A4RN-01A-12D-A28Q-01
TCGA-N5-A4RO-01A-11D-A28Q-01
TCGA-N5-A4RS-01A-11D-A28Q-01
TCGA-N5-A4RT-01A-11D-A28Q-01
TCGA-N5-A4RU-01A-31D-A28Q-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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