wxs Copy number analysis (GISTIC2)

Overview

Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.23.

Summary

There were 90 tumor samples used in this analysis: 19 significant arm-level results, 20 significant focal amplifications, and 39 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 - 20 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband	Q value	Residual Q value	Wide Peak Boundaries	# Genes in Wide Peak
17q12	8.5008e-25	6.9483e-22	chr17:37840849-38024682	7
11q13.3	9.5895e-14	1.0005e-13	chr11:69062821-69931685	7
13q12.11	1.3967e-10	1.3967e-10	chr13:21729218-21746838	1
1q32.2	2.348e-09	2.348e-09	chr1:207700315-207737384	1
8q24.21	2.3265e-07	2.3265e-07	chr8:126448247-130762817	21
8p11.23	8.2766e-06	8.2766e-06	chr8:36925105-37914779	10
16p11.2	1.8508e-05	1.8508e-05	chr16:28607103-28631468	2
12p13.33	0.00010623	0.00010623	chr12:1-905787	10
15q26.3	0.00016591	0.00016591	chr15:102513105-102531392	2
11p13	0.00053432	0.00057408	chr11:34502308-35482889	8
2q31.2	0.0019264	0.0019264	chr2:179296774-179319304	2
17q23.1	1.9045e-10	0.0021019	chr17:57304646-62883017	80
10p14	0.0028976	0.0028976	chr10:7633142-11057294	12
9p24.3	0.0039692	0.0039692	chr9:1-30280	0 [FAM138C]
20q13.31	0.0064822	0.0064822	chr20:51589804-56728689	36
19q13.33	0.082466	0.082466	chr19:49825803-50362597	37
19p13.11	0.10805	0.10805	chr19:17457756-19115356	59
1p36.33	0.12541	0.12541	chr1:1-3311105	77
4q13.3	0.14196	0.14196	chr4:74123981-75682509	23
3q26.32	0.23442	0.23442	chr3:161220077-198022430	257

Genes in Wide Peak

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

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

Genes
ERBB2
GRB7
MIEN1
PGAP3
IKZF3
ZPBP2
MIR4728

Genes in Wide Peak

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

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

Genes
CCND1
FGF4
ANO1
ORAOV1
FGF19
MYEOV
FGF3

Genes in Wide Peak

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

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

Genes
SKA3

Genes in Wide Peak

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

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

Genes
CR1

Genes in Wide Peak

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

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

Genes
MYC
GSDMC
FAM84B
TRIB1
RN7SKP226
POU5F1B
MIR1207
MIR1208
MIR1205
RN7SKP206
CCDC26
LINC00861
CASC8
CCAT1
PVT1
LINC00977
PCAT2
PCAT1
TMEM75
MIR3686
RN7SL590P

Genes in Wide Peak

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

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

Genes
GPR124
BRF2
PROSC
ERLIN2
RAB11FIP1
GOT1L1
ZNF703
EIF4EBP1
ADRB3
RN7SL709P

Genes in Wide Peak

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

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

Genes
SULT1A1
SULT1A2

Genes in Wide Peak

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

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

Genes
KDM5A
SLC6A13
WNK1
SLC6A12
IQSEC3
CCDC77
B4GALNT3
NINJ2
FAM138D
RNU4ATAC16P

Genes in Wide Peak

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

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

Genes
WASH3P
DDX11L9

Genes in Wide Peak

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

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

Genes
CD44
PDHX
SLC1A2
EHF
ELF5
APIP
PAMR1
MIR1343

Genes in Wide Peak

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

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

Genes
PRKRA
DFNB59

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q23.1.

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

Genes
CD79B
DDX5
BRIP1
CLTC
SCN4A
CYB561
MRC2
VMP1
APPBP2
HEATR6
PSMC5
METTL2A
DHX40
TUBD1
RPS6KB1
INTS2
MED13
CCDC47
FTSJ3
SMARCD2
ICAM2
SMURF2
TBX2
TBX4
TACO1
TEX2
DCAF7
GH2
CSH1
LIMD2
C17orf64
BCAS3
PTRH2
TLK2
GDPD1
ACE
CA4
USP32
PPM1D
TANC2
EFCAB3
KCNH6
MARCH10
YPEL2
LRRC37A3
ERN1
C17orf82
TBC1D3P2
RNFT1
DDX42
MAP3K3
MIR21
SNORD104
CSHL1
MIR633
CSH2
RPL12P38
PLEKHM1P
C17orf72
snoU13\|ENSG00000238799.1
RN7SL606P
TCAM1P
RN7SL800P
SCARNA20\|ENSG00000252577.1
NACA2
POLG2
CEP95
GH1
RN7SL409P
MIR4729
MIR4737
RN7SL448P
RN7SL805P
ACE
RN7SL404P
MIR3064
STRADA
MIR5047
SNORA76\|ENSG00000266402.2
MILR1

Genes in Wide Peak

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

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

Genes
GATA3
CELF2
ITIH5
ITIH2
KIN
ATP5C1
TAF3
RNA5SP299
SFTA1P
LINC00710
LINC00709
LINC00708

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.31.

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

Genes
CYP24A1
RTFDC1
SPO11
CBLN4
BCAS1
TFAP2C
AURKA
CASS4
PFDN4
DOK5
CSTF1
BMP7
RAE1
MC3R
GCNT7
CTCFL
FAM210B
FAM209A
PMEPA1
C20orf85
PCK1
ZBP1
RBM38
ZNF217
TSHZ2
RN7SKP184
FAM209B
RNA5SP487
snoU13\|ENSG00000238294.1
RN7SL170P
RNU4ATAC7P
U3\|ENSG00000252536.1
MTRNR2L3
MIR4532
MIR4756
MIR4325

Genes in Wide Peak

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

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

Genes
FUZ
SLC6A16
TEAD2
FLT3LG
FCGRT
PIH1D1
SLC17A7
CD37
DKKL1
PTOV1
MED25
BCL2L12
IRF3
PRMT1
RRAS
PRRG2
SCAF1
PRR12
TSKS
RPS11
PTH2
RPL13A
NOSIP
RCN3
CCDC155
ALDH16A1
CPT1C
AP2A1
SNORD33\|ENSG00000199631.1
SNORD35A
SNORD35B
SNORD32A
SNORD34
MIR150
ADM5
MIR5088
MIR4749

Genes in Wide Peak

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

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

Genes
JAK3
ELL
UPF1
C19orf60
CRLF1
CCDC124
HOMER3
SUGP2
IL12RB1
MAST3
RPL18A
SLC5A5
ARRDC2
PIK3R2
RAB3A
PDE4C
ISYNA1
CRTC1
COMP
COPE
DDX49
TMEM59L
KXD1
FKBP8
GDF1
PLVAP
BST2
SLC27A1
COLGALT1
PGLS
FCHO1
UNC13A
MAP1S
SSBP4
GDF15
PGPEP1
KIAA1683
LSM4
JUND
MVB12A
FAM129C
KLHL26
NXNL1
LRRC25
B3GNT3
TMEM221
SNORA68\|ENSG00000207166.1
IFI30
UBA52
CERS1
RN7SL513P
RN7SL70P
INSL3
RNA5SP468
MPV17L2
RN7SL155P
MIR3189
MIR3188
PIK3R2

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
AFM
CXCL2
AFP
PF4V1
AREG
CXCL6
EREG
ANKRD17
ALB
CXCL3
CXCL5
PPBP
PF4
MTHFD2L
CXCL1
IL8
RASSF6
BTC
EPGN
AREGB
SNORA3\|ENSG00000221639.1
RN7SL218P
PPBPP2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.32.

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

Genes
TFRC
BCL6
PIK3CA
LPP
EIF4A2
SOX2
ETV5
SEC62
SLC7A14
CLDN11
LSG1
DCUN1D1
MCF2L2
USP13
ATP11B
DGKG
TNK2
TP63
IGF2BP2
MAP3K13
ST6GAL1
FNDC3B
PLD1
DLG1
MCCC1
LAMP3
MYNN
MECOM
SI
FETUB
DNAJB11
LEPREL1
THPO
CHRD
EHHADH
TBCCD1
KNG1
HRG
CLDN16
BCHE
SERPINI2
PDCD10
LRRC31
FGF12
HES1
ACAP2
ECT2
FXR1
GNB4
IQCG
NCBP2
PEX5L
ABCC5
KLHL24
CLCN2
EIF4G1
PIGZ
SENP5
GHSR
TNFSF10
ZNF639
SLITRK3
FYTTD1
MASP1
ATP13A4
HRASLS
ATP13A3
RTP4
ACTL6A
NDUFB5
MRPL47
TRA2B
SKIL
NCEH1
SPATA16
TMEM44
KIAA0226
CCDC39
TM4SF19
MUC4
EIF2B5
AHSG
ECE2
VWA5B2
CCDC50
TNIK
VPS8
SST
DVL3
AP2M1
ABCF3
PCYT1A
BDH1
CLDN1
SERPINI1
PRKCI
EIF5A2
SLC2A2
RPL22L1
TTC14
YEATS2
POLR2H
CAMK2N2
LIPH
TMEM41A
SENP2
C3orf65
RFC4
RPL39L
ZDHHC19
SLC51A
UBXN7
RNF168
PIGX
MFI2
ZBBX
NLGN1
MFN1
KCNMB3
LRRC34
LRRC15
KLHL6
ZMAT3
PHC3
GPR160
GOLIM4
XXYLT1
NRROS
CEP19
FBXO45
WDR49
RTP1
PSMD2
FAM131A
PARL
B3GNT5
MUC20
MAGEF1
TBL1XR1
NAALADL2
HTR3C
GP5
CPN2
PAK2
MB21D2
MAP6D1
ADIPOQ
OTOL1
EPHB3
RPL35A
PP13439
PPP1R2
ACTRT3
FAM43A
SDHAP1
LMLN
WDR53
LRCH3
HTR3E
HTR3D
TMEM212
SAMD7
C3orf70
ATP13A5
TPRG1
LRRIQ4
OSTN
UTS2B
APOD
IL1RAP
KCNMB2
TMEM207
RTP2
OPA1
SNORA63\|ENSG00000199363.1
RNA5SP150
SNORA18\|ENSG00000200288.1
SNORA63\|ENSG00000200320.1
SNORA72\|ENSG00000200355.1
SNORA63\|ENSG00000200418.1
SNORA63\|ENSG00000201229.1
U8\|ENSG00000201810.1
RNA5SP149
SNORA25\|ENSG00000201957.1
RNA5SP151
LINC00501
GMNC
DNAJC19
EGFEM1P
MIR570
MIR28
MIR551B
MIR569
SNORD66\|ENSG00000212158.1
TCTEX1D2
CRYGS
SMCO1
LINC00887
ALG3
MIR922
MIR944
MIR1224
MIR1263
SNORA81\|ENSG00000221420.2
MIR720
RNY5P3
RN7SKP222
RN7SKP296
LINC00885
ANKRD18DP
LINC00578
LINC00884
CYP2AB1P
FAM157A
snoU13\|ENSG00000238359.1
snoU13\|ENSG00000238398.1
snoU13\|ENSG00000238491.1
snoU13\|ENSG00000238902.1
SNORD2\|ENSG00000238942.1
snoU13\|ENSG00000239093.1
snoU13\|ENSG00000239096.1
snoU13\|ENSG00000239141.1
snoU13\|ENSG00000239146.1
LINC00888
CT64
RN7SL434P
LINC00969
RN7SL215P
RN7SL229P
RN7SL738P
RN7SL141P
RN7SL447P
RN7SL36P
SNORA4\|ENSG00000251730.1
RN7SKP298
RN7SKP52
RN7SKP265
RNA5SP147
RNA5SP148
RNU6ATAC24P
RN7SKP234
RN7SKP40
SNORA81\|ENSG00000253092.1
PYDC2
SNORA4\|ENSG00000263776.1
MIR4448
MIR4789
RN7SL486P
MIR3137
MIR548AQ
MIR4797
RN7SL703P
RN7SL637P
RN7SL773P
TERC
snoU13\|ENSG00000271842.1
U4\|ENSG00000272359.1

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 - 39 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
11q23.3	1.4242e-15	1.4242e-15	chr11:117069586-117109314	2
5p13.1	5.5206e-15	5.5206e-15	chr5:38452155-38942516	2
8p23.1	1.2206e-14	1.2206e-14	chr8:1-13948212	115
15q15.1	1.6415e-16	4.2136e-13	chr15:41828850-41968869	1
12p13.33	5.9867e-11	5.5604e-11	chr12:1-1023057	10
16q21	1.3246e-13	5.5604e-11	chr16:58540382-58659746	4
17p12	1.6438e-09	1.6438e-09	chr17:15929804-16105441	1
15q24.2	1.3933e-13	4.0884e-09	chr15:75503089-75594075	4
6q25.3	1.8679e-07	1.8679e-07	chr6:160921812-161412940	2
4p15.2	6.7999e-07	6.7999e-07	chr4:25270201-25658484	2
1p36.11	1.4708e-10	1.1943e-06	chr1:13333-31405348	502
11p15.5	2.0128e-06	1.8176e-06	chr11:1-460289	17
9p21.3	1.4781e-05	1.4781e-05	chr9:21028241-26842296	32
19p13.2	1.3307e-07	1.789e-05	chr19:8931985-9204863	2
16q22.2	2.0248e-14	2.1657e-05	chr16:72049711-72130909	3
1p36.32	5.5206e-15	5.53e-05	chr1:13333-3379647	76
2q31.2	5.8629e-05	0.00011883	chr2:179259165-179337713	2
17q21.32	0.0001148	0.00011883	chr17:45110602-45299174	3
9q21.32	0.00016407	0.00015123	chr9:84498741-85597589	6
19q13.33	0.00015123	0.00015123	chr19:48387045-48556405	3
2q13	8.6293e-05	0.00017304	chr2:114028195-114475438	6
7q22.1	3.4654e-05	0.00024529	chr7:100488488-100730591	6
18q11.1	0.0014285	0.0015218	chr18:14539623-19031111	4
13q12.11	2.4274e-06	0.0015735	chr13:21620168-21751053	4
4q12	0.0021566	0.0021566	chr4:48040967-52862332	10
14q32.33	0.0060721	0.0060721	chr14:63483675-107349540	467
3p21.2	0.0074789	0.0072869	chr3:43774017-84689615	349
19p13.3	9.6381e-06	0.018439	chr19:1-2024156	78
21q22.11	0.023471	0.022018	chr21:31738239-33478933	6
5q13.3	0.037114	0.048643	chr5:59680780-108133881	229
10q24.32	0.053412	0.050343	chr10:104836028-105038942	1
13q14.12	0.00042373	0.050343	chr13:44971380-46276999	17
10p11.21	0.067169	0.065817	chr10:33604079-35417465	4
2p16.2	0.079129	0.079665	chr2:54045121-54214929	4
7q11.23	0.00016591	0.093922	chr7:74173091-74299961	2
13q12.11	5.3526e-06	0.11158	chr13:1-20541403	15
12q24.31	0.1384	0.13606	chr12:98850352-133851895	356
1p13.2	0.018439	0.36311	chr1:86146505-117508636	249
19p13.3	9.6381e-06	1	chr19:1-59128983	1616

Genes in Wide Peak

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

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

Genes
PCSK7
TAGLN

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5p13.1.

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

Genes
LIFR
MIR3650

Genes in Wide Peak

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

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

Genes
MYOM2
FDFT1
ANGPT2
ERI1
MTMR9
ERICH1
ARHGEF10
BLK
GATA4
FAM86B2
MCPH1
MFHAS1
FBXO25
TDH
FAM167A
NEIL2
LONRF1
AGPAT5
CTSB
DLC1
C8orf48
DEFA5
DEFA4
DEFA6
DEFB1
SPAG11B
LINC00208
XKR6
SOX7
C8orf74
DEFB4A
ZNF596
TNKS
PPP1R3B
FAM86B3P
MSRA
OR4F21
KBTBD11
DEFB104A
DEFB103A
DEFB104B
DEFB103B
DEFB4B
SLC35G5
SPAG11A
TDRP
SGK223
CLN8
CSMD1
RP1L1
C8orf12
PRSS55
FAM86B1
XKR5
DEFB105A
DEFB107A
DEFB106A
DEFB105B
DEFB106B
DLGAP2
DEFB107B
DEFB134
DEFB135
DEFB136
DEFA1
SNORA70\|ENSG00000206661.1
SNORA70\|ENSG00000207244.1
MIR598
MIR597
MIR596
RNA5SP252
ZNF705D
FAM90A24P
ZNF705B
ZNF705G
FAM66B
MIR548I3
RNA5SP251
RN7SKP159
USP17L2
RPL23AP53
FAM66E
FAM66A
DEFB130\|ENSG00000232948.1
DEFB130\|ENSG00000233050.1
LINC00529
snoU13\|ENSG00000238496.1
snoU13\|ENSG00000239065.1
DEFA3
DEFA1B
RN7SL318P
RN7SL293P
KIAA1456
RNA5SP253
RNA5SP255
RNA5SP254
U3\|ENSG00000252543.1
SNORD112\|ENSG00000252565.1
LINC00599
PRSS51
FAM85B
CLDN23
ALG1L13P
PINX1
FAM66D
C8orf49
LINC00681
SOX7
MIR4660
RN7SL178P
MIR4286
MIR5692A2
RN7SL872P
MIR4659A
LRLE1

Genes in Wide Peak

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

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

Genes
TYRO3

Genes in Wide Peak

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

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

Genes
KDM5A
SLC6A13
WNK1
SLC6A12
IQSEC3
CCDC77
B4GALNT3
NINJ2
FAM138D
RNU4ATAC16P

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q21.

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

Genes
SETD6
SNORA50\|ENSG00000206952.2
SNORA46\|ENSG00000207493.1
snoU13\|ENSG00000239121.1

Genes in Wide Peak

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

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

Genes
RN7SL442P

Genes in Wide Peak

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

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

Genes
GOLGA6D
GOLGA6C
RN7SL489P
RN7SL327P

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q25.3.

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

Genes
PLG
LPA

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p15.2.

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

Genes
ANAPC4
ZCCHC4

Genes in Wide Peak

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

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

Genes
PAX7
RPL22
SDHB
ARID1A
PRDM16
TNFRSF14
MDS2
FGR
STPG1
NIPAL3
KDM1A
DNAJC11
E2F2
CDK11A
NADK
MASP2
FAM76A
TCEB3
LYPLA2
CLCN6
RUNX3
TNFRSF1B
FBXO42
PQLC2
THAP3
VPS13D
H6PD
VAMP3
PER3
UTS2
TNFRSF9
AKR7A2
MRTO4
KIF1B
SZRD1
PITHD1
CROCC
PIGV
PTPRU
SPEN
PRKCZ
KCNAB2
HES2
CDC42
EPHA8
ENO1
ARHGEF10L
EIF4G3
RAP1GAP
CAPZB
GNB1
SDF4
TP73
CROCCP3
PLOD1
ASAP3
SLC9A1
NUDC
MUL1
USP48
ACOT7
DVL1
DNAJC16
MORN1
CEP104
WRAP73
ICMT
CHD5
PHF13
ERRFI1
PARK7
OPRD1
SRSF4
MECR
SRM
FBXO2
FBXO6
MAD2L2
KIAA2013
MFN2
MIIP
PRAMEF1
PRAMEF12
PRDM2
AGMAT
PLEKHM2
ZBTB17
PADI2
MFAP2
ACTL8
IGSF21
PLA2G2D
KIF17
ECE1
HMGCL
GALE
ID3
RCAN3
SYF2
C1orf63
STMN1
MTFR1L
MAN1C1
RPS6KA1
DHDDS
RPA2
PPP1R8
STX12
TAF12
NPPB
UBIAD1
TARDBP
TNFRSF8
PRAMEF2
HNRNPR
ZNF436
DNAJC8
AHDC1
IFI6
CPSF3L
AUNIP
EMC1
PLA2G5
UBR4
HP1BP3
CEP85
ARHGEF16
LRRC47
SESN2
SMPDL3B
ATPIF1
MED18
THEMIS2
UBE4B
CASZ1
ACAP3
C1orf159
CA6
NPHP4
NR0B2
LIN28A
FBXO44
RSG1
CASP9
EPHB2
SRRM1
SLC2A5
RERE
MMEL1
C1orf222
CELA2A
PADI3
FHAD1
PADI1
EPHA2
ARHGEF19
EFHD2
PEX14
PGD
MYOM3
SH3BGRL3
CNKSR1
RPL11
IL22RA1
ZNF593
MAP3K6
FCN3
GPN2
SYTL1
WDTC1
CELA3A
NBPF3
HSPG2
PLCH2
NECAP2
C1orf158
PRAMEF15
FAM213B
PANK4
PEX10
RER1
SKI
LDLRAP1
PAFAH2
EXTL1
SLC30A2
TRIM63
GRHL3
UBXN11
TPRG1L
XKR8
EYA3
WASF2
FAM46B
RNF207
GPR153
NBL1
HTR6
PLA2G2F
VWA5B1
CDA
PINK1
EPB41
C1QC
PADI4
ATP13A2
ALDH4A1
DFFA
ATAD3B
SSU72
UBE2J2
NOL9
KLHL21
GMEB1
SLC45A1
SEPN1
CTRC
LZIC
RBP7
FBLIM1
TMEM82
SLC25A34
AKR7A3
DRAXIN
PDPN
LRRC38
DHRS3
MATN1
LAPTM5
SDC3
TMCO4
UBXN10
CAMK2N1
ALPL
WNT4
TTLL10
SCNN1D
MXRA8
C1orf86
MEGF6
CCDC27
PTAFR
CD52
CLIC4
DFFB
LUZP1
ACTRT2
CALML6
OTUD3
TAS1R3
PUSL1
IFFO2
CLSTN1
PIK3CD
SLC25A33
SPSB1
PLEKHG5
TMEM51
CAMTA1
ANGPTL7
EXOSC10
C1QB
C1QA
MINOS1
NMNAT1
HSPB7
TAS1R1
HES3
CD164L2
PDIK1L
NPPA
C1orf127
APITD1
C1orf172
AURKAIP1
SFN
B3GALT6
ZNF683
AIM1L
MTHFR
LINC00982
AGTRAP
FAM87B
CTNNBIP1
TMEM52
RNF186
TAS1R2
KLHDC7A
RCC2
FUCA1
HNRNPCL1
VWA1
HTR1D
C1orf200
TRNAU1AP
RCC1
GPR157
GPR3
PRAMEF8
PAQR7
FAM43B
TMEM50A
C1orf64
FAM132A
NCMAP
ZBTB40
CLCNKB
OR4F16
IFNLR1
FAM131C
OR4F5
TMEM222
CLCNKA
MST1L
TNFRSF4
TNFRSF18
RHD
ESPN
SPATA21
PRAMEF10
PLEKHN1
ISG15
SAMD11
C1orf170
GABRD
LDLRAD2
KLHL17
PLA2G2C
RAB42
AGRN
PLA2G2A
HES4
SRSF10
RHCE
CATSPER4
PLA2G2E
TMEM201
CNR2
NOC2L
AADACL3
PNRC2
KAZN
SLC35E2B
MMP23B
SH2D5
AJAP1
SLC2A7
FAM110D
DDI2
MIB2
ATAD3A
HES5
SNHG12
YTHDF2
GPATCH3
MTOR
HMGN2
C1orf174
MIR429
SNORA73B
RN7SKP269
PHACTR4
ZDHHC18
TMEM57
TCEA3
C1orf134
C1orf195
PRAMEF20
PRAMEF17
PRAMEF19
PRAMEF14
PRAMEF21
PRAMEF16
PRAMEF18
PRAMEF13
PRAMEF9
PRAMEF5
PRAMEF3
PRAMEF22
PRAMEF7
PRAMEF11
AADACL4
PTCHD2
ZBTB48
TMEM240
TMEM88B
MIR200A
MIR200B
MIR551A
MIR34A
AKR7L
RSC1A1
CELA2B
TNFRSF25
SLC35E2
LACTBL1
CROCCP2
C1orf167
TTC34
ATAD3C
LINC00339
CELA3B
NBPF1
SNORA77\|ENSG00000221083.1
RNU6ATAC27P
RNU6ATAC18P
SNORD99
MIR1290
MIR1256
CCNL2
RN7SKP91
RNA5SP41
GLTPD1
LINC00337
LINC00115
C1orf234
U1\|ENSG00000228549.2
C1orf233
FAM41C
PRAMEF6
U1\|ENSG00000233421.3
ANKRD65
SMIM1
OR4F29
ANO7P1
RNF223
FAM138A
snoU13\|ENSG00000238316.1
snoU13\|ENSG00000238538.1
MIR1976
snoU13\|ENSG00000238771.1
snoU13\|ENSG00000238818.1
snoU13\|ENSG00000238821.1
snoU13\|ENSG00000238889.1
snoU13\|ENSG00000238986.1
snoU13\|ENSG00000239020.1
snoU13\|ENSG00000239027.1
SNORA59A
snoU13\|ENSG00000239166.1
RN7SL277P
RN7SL559P
RN7SL165P
CORT
SNHG3
MRPL20
RN7SL304P
PRAMEF4
RN7SL614P
RN7SL649P
RN7SL679P
DDOST
RN7SL532P
CDK11B
C1orf213
SCARNA21\|ENSG00000251866.1
SCARNA17\|ENSG00000252190.1
SCARNA16\|ENSG00000252404.1
SCARNA18\|ENSG00000252691.1
SCARNA24\|ENSG00000252777.1
SCARNA1
RNA5SP40
SNORA70\|ENSG00000252969.1
SCARNA11\|ENSG00000253085.1
TMEM200B
TRNP1
PADI6
RN7SL768P
MIR4632
MIR3115
MIR3675
RN7SL186P
RN7SL386P
MIR4253
MIR3917
MIR4689
RN7SL657P
MIR4417
RN7SL24P
MIR4425
RN7SL421P
RN7SL731P
MIR4420
MIR1273D
MIR378F
RN7SL451P
RN7SL490P
RN7SL85P
MIR4252
RN7SL729P
MIR4684
MIR5697
MIR4695
RN7SL721P
RN7SL574P
RN7SL501P
RN7SL857P
MIR4418
MIR3972
MIR4419A
ESPNP
RNU11
snoU13\|ENSG00000271794.1

Genes in Wide Peak

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

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

Genes
SIRT3
IFITM3
ATHL1
NLRP6
ODF3
BET1L
RIC8A
B4GALNT4
PKP3
ANO9
SIGIRR
IFITM2
PSMD13
IFITM1
SCGB1C1
IFITM5
RN7SL838P

Genes in Wide Peak

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

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

Genes
MTAP
ELAVL2
IFNA6
IFNA8
IFNA21
IFNA5
CDKN2B
IFNA16
CDKN2A
IFNB1
MIR31HG
DMRTA1
IFNW1
IFNE
IFNA10
IFNA2
IFNA1
KLHL9
TUSC1
MIR31
IZUMO3
IFNA7
RN7SKP120
RMRPP5
C9orf53
IFNA14
IFNA13
IFNA17
IFNA4
RN7SL151P
SNORA31\|ENSG00000252580.1
SNORD39\|ENSG00000264379.1

Genes in Wide Peak

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

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

Genes
MBD3L1
MUC16

Genes in Wide Peak

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

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

Genes
TXNL4B
HP
HPR

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
PRKRA
DFNB59

Genes in Wide Peak

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

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

Genes
CDC27
snoU13\|ENSG00000252088.1
RN7SL270P

Genes in Wide Peak

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

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

Genes
SPATA31D3
SPATA31D4
SNORD95\|ENSG00000200969.1
SPATA31D1
SPATA31D5P
RNA5SP287

Genes in Wide Peak

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

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

Genes
CABP5
ELSPBP1
BSPH1

Genes in Wide Peak

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

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

Genes
CBWD2
RABL2A
WASH2P
FOXD4L1
FAM138B
RPL23AP7

Genes in Wide Peak

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

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

Genes
MUC17
MUC3A
MUC12
RN7SKP54
MUC3A
RN7SL549P

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q11.1.

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

Genes
ROCK1
ANKRD30B
SNORD23\|ENSG00000221139.1
RN7SL662P

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
SAP18
SKA3
SNORD27\|ENSG00000252128.1
RN7SL80P

Genes in Wide Peak

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

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

Genes
TXK
FRYL
SLAIN2
OCIAD1
CWH43
DCUN1D4
TEC
OCIAD2
SLC10A4
ZAR1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q32.33.

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

Genes
GOLGA5
DICER1
TCL1A
TRIP11
BCL11B
AKT1
TSHR
GPHN
TCL6
MAP3K9
POMT2
BTBD7
UBR7
ANGEL1
CCDC88C
NRXN3
ZNF839
SLC39A9
FUT8
CYP46A1
TDP1
SPATA7
FOXN3
SYNE2
PLEKHH1
GALC
ADCK1
ATXN3
EML1
KIF26A
ATG2B
SPTB
PTPN21
VASH1
SEL1L
RDH11
ACTN1
ZFYVE26
MPP5
MARK3
PPP2R5C
PSEN1
MOK
HSP90AA1
EXD2
ARG2
PPP1R13B
OTUB2
DDX24
ZBTB25
RCOR1
GPATCH2L
PAPOLA
CCNK
CEP170B
KCNK10
ATP6V1D
PLEK2
PIGH
C14orf166B
VTI1B
GSTZ1
TMED8
SAMD15
AHSA1
ISM2
SPTLC2
RIN3
LGMN
ALKBH1
SNW1
CHGA
ITPK1
GALNT16
ASB2
CEP128
ERH
KIAA0247
SRSF5
SLC10A1
EIF5
SERPINA4
SLC8A3
ZFYVE21
MTHFD1
ZC3H14
PCNX
BDKRB1
GSKIP
VRK1
PSMC1
PAPLN
RPS6KA5
SMEK1
YY1
CINP
YLPM1
DCAF4
PROX2
VSX2
FCF1
PGF
IFI27L2
CCDC176
NEK9
ACYP1
IFT43
NPC2
DNAL1
IRF2BPL
ACOT2
LTBP2
AREL1
MLH3
TTLL5
FLVCR2
ABCD4
DLST
PPP4R4
TGFB3
ZC2HC1C
SLIRP
RBM25
ALDH6A1
GPR68
ESRRB
EIF2B2
NRDE2
COQ6
ZNF410
MAX
KLC1
XRCC3
RHOJ
HSPA2
ZBTB1
SGPP1
PLEKHG3
TRAF3
C14orf1
GSC
C14orf159
UNC79
NUMB
CATSPERB
VRTN
COX16
TTC9
MED6
EIF2S1
ADAM20
ADAM21
RDH12
DCAF5
RAB15
WDR89
ESR2
STON2
EFCAB11
GPR65
PTGR2
JDP2
AK7
FAM181A
SLC24A4
FBLN5
SERPINA10
C14orf79
WARS
SLC25A47
WDR20
VIPAS39
KCNK13
TMEM251
PPP2R5E
ELMSAN1
FAM161B
BATF
ANKRD9
C14orf2
TDRD9
GTF2A1
EML5
TTC8
TMEM63C
NGB
NOXRED1
PPP1R36
ZFYVE1
ISCA2
TTC7B
TC2N
CPSF2
MOAP1
IFI27L1
IFI27
SERPINA12
CLMN
AMN
CKB
TRMT61A
BAG5
ASPG
PLD4
DEGS2
BDKRB2
SERPINA9
SERPINA6
C14orf142
FOS
TMED10
CDCA4
FAM71D
LINC00521
PRIMA1
PLEKHD1
GPX2
SYNE3
WDR25
C14orf177
PNMA1
ZDHHC22
ACOT4
PACS2
GPHB5
ZBTB42
AKAP5
RAD51B
HHIPL1
GLRX5
RGS6
CRIP2
MTA1
BEGAIN
SYNDIG1L
GPR132
SETD3
NDUFB1
NUDT14
ACOT1
C14orf180
BTBD6
JAG2
TMEM121
SIVA1
BRF1
FLRT2
ADSSL1
TNFAIP2
C14orf80
DLK1
AHNAK2
ZFP36L1
SERPINA11
ENTPD5
HEATR4
LINC00221
SERPINA13P
COX8C
SERPINA5
MIR494
SERPINA3
LINC00523
EVL
LINC00238
TECPR2
DYNC1H1
SLC25A29
SERPINA1
DIO3
SIPA1L1
C14orf178
TMEM229B
RPS6KL1
CALM1
SMOC1
CDC42BPB
KIAA1737
MIR380
MIR345
MIR370
MIR412
MIR377
MIR381
MIR369
MIR323A
MIR342
MIR379
MIR410
MIR409
MIR411
MIR337
RNA5SP388
RNA5SP389
U3\|ENSG00000200042.1
SNORD113\|ENSG00000200150.1
RN7SKP255
U3\|ENSG00000200693.1
RN7SKP107
SNORD113\|ENSG00000201036.1
RNA5SP387
SNORA32\|ENSG00000201384.1
SNORD113\|ENSG00000201500.1
SNORD113\|ENSG00000201710.1
SNORD51\|ENSG00000202275.1
MIR539
INF2
EXOC3L4
CCDC85C
LIN52
ACOT6
DPF3
U3\|ENSG00000206761.1
SNORD56B
MIR487A
MIR203
MIR433
MIR544A
MIR127
MIR655
MIR382
MIR495
MIR299
MIR487B
MIR625
MIR654
MIR136
MIR656
MIR496
MIR154
MIR493
MIR134
MIR431
MIR323B
MIR485
DIO2
MIR770
MIR758
IGHA2
IGHE
IGHG4
IGHG2
IGHA1
IGHG1
IGHG3
IGHD
IGHM
IGHJ6
IGHJ2
IGHJ1
MIR543
SNORA46\|ENSG00000212371.1
CRIP1
TCL1B
SYNJ2BP
MEG3
MIR300
MIR889
MIR541
MIR1193
SNORA11\|ENSG00000221060.1
SNORA11B
SNORA79\|ENSG00000221303.1
MIR548H1
MIR1197
MIR1260A
SNORD113\|ENSG00000222095.1
SNORD113\|ENSG00000222185.1
SNORA7\|ENSG00000222604.1
RN7SKP17
RN7SKP108
MEG9
LINC00618
TEX22
KIAA0125
C14orf132
RD3L
C14orf144
LINC00226
LINC00341
LINC00642
ADAM6
ADAM21P1
snoU13\|ENSG00000238330.1
RNU6ATAC28P
snoU13\|ENSG00000238776.1
snoU13\|ENSG00000238853.1
snoU13\|ENSG00000238972.1
snoU13\|ENSG00000238978.1
snoU13\|ENSG00000239061.1
RN7SL546P
RN7SL213P
RN7SL530P
IGHJ4
RN7SL587P
RN7SL472P
RN7SL710P
RN7SL77P
RN7SL586P
RN7SL369P
RN7SL714P
RN7SL683P
IGHJ5
IGHJ3
RN7SL634P
RN7SL108P
RN7SL523P
RN7SL706P
C14orf64
SNHG10
LINC00617
LINC00605
SNORD112\|ENSG00000251769.1
SNORD112\|ENSG00000251918.1
SNORD112\|ENSG00000251949.1
SNORD112\|ENSG00000252009.1
RNU4ATAC14P
SNORD112\|ENSG00000252144.1
SCARNA13
RNU3P3
U3\|ENSG00000252792.1
SCARNA20\|ENSG00000252800.1
SNORD112\|ENSG00000252873.1
RN7SKP92
RTL1
C14orf169
CCDC177\|ENSG00000255994.1
APOPT1
CRIP1
FNTB
CHURC1
MEG8
DIO3OS
LINC00638
DKFZP434O1614
LINC00637
MIR381HG
TMEM179
LINC00524
LINC00911
ADAM20P1
LINC00677
RN7SL224P
RN7SL747P
MIR3173
MIR4505
MIR376A1
RN7SL540P
MIR151B
MIR4710
MIR4709
MIR4506
MIR5694
MIR4309
RN7SL506P
MIR2392
MIR4706
RN7SL356P
RN7SL137P
MIR4708
CCDC177\|ENSG00000267909.1
FKSG61
MIR376C
MIR665
U6\|ENSG00000272439.1
MIR432
SNORA28

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p21.2.

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

Genes
FOXP1
BAP1
PBRM1
SETD2
MITF
FHIT
SEMA3F
RBM5
RBM6
ZMYND10
CACNA2D2
CELSR3
UQCRC1
PHF7
SEMA3G
NISCH
STAB1
LARS2
SEMA3B
LTF
CHDH
GLT8D1
ALAS1
PARP3
MAP4
ITIH4
ITIH1
IL17RB
RHOA
HYAL2
RASSF1
IP6K2
EXOSC7
PTPN23
DOCK3
C3orf18
KIF9
PCBP4
CNTN3
SELK
ACTR8
WNT5A
PFKFB4
COL7A1
PRKAR2A
USP4
GNAT1
GNAI2
HYAL1
TUSC2
NPRL2
CYB561D2
C3orf14
GBE1
FRMD4B
CSPG5
KLHL18
SCAP
HEMK1
CISH
MAPKAPK3
RRP9
ABHD14B
DNAH1
TNNC1
SPCS1
NEK4
PDZRN3
ACKR5
CCR2
TMEM115
DHX30
FLNB
PTPRG
IL17RD
SHQ1
SLC25A26
UBA3
ARL6IP5
TMF1
LRIG1
LRTM1
LIMD1
ZNF660
AMT
TCTA
NICN1
UCN2
VPRBP
MANF
MAGI1
FEZF2
CACNA1D
CACNA2D3
APPL1
CCR5
NBEAL2
CCDC12
PTH1R
MYL3
RPL29
ITIH3
DCP1A
KBTBD8
FAM19A4
EOGT
LMOD3
EIF4E3
PROK2
RYBP
PPP4R2
CADPS
SYNPR
C3orf49
THOC7
ATXN7
PSMD6
PRICKLE2
ADAMTS9
HESX1
SLMAP
RPP14
ABHD6
DNASE1L3
C3orf67
KIAA1143
KIF15
TGM4
ZDHHC3
CDCP1
CLEC3B
SLC6A20
LZTFL1
FYCO1
CCR1
RTP3
LRRC2
ELP6
TKT
PRKCD
RFT1
SFMBT1
GNL3
FAM208A
ARHGEF3
CDC25A
CAMP
ZNF589
FBXW12
PLXNB1
CCDC51
ATRIP
SHISA5
BSN
APEH
RNF123
CAMKV
MON1A
MST1R
RAD54L2
TEX264
GRM2
DUSP7
POC1A
PPM1M
WDR82
GLYCTK
NT5DC2
SMIM4
PDHB
PXK
KCTD6
ACOX2
FAM107A
ARF4
ROBO1
TMEM42
ZNF35
GPR27
LAMB2
USP19
QARS
NME6
CXCR6
SUCLG2
FRG2C
GXYLT2
TLR9
IQCF1
DAG1
CCDC36
SMARCC1
MST1
GMPPB
XCR1
CCR9
TOPAZ1
DENND6A
PDE12
DNAH12
AMIGO3
IP6K1
CCDC71
ARIH2
IMPDH2
ALS2CL
PRSS42
NDUFAF3
DALRD3
WDR6
P4HTM
SLC25A20
ZNF852
TCAIM
LSMEM2
RBM15B
CCDC66
GPR62
TMIE
UBA7
TMEM89
CCR3
FAM19A1
TRAIP
IQCF2
ROBO2
ZNF445
FAM212A
KLHDC8B
ZNF501
ZNF197
SPATA12
HYAL3
CDHR4
ERC2
PRSS45
C3orf62
SLC38A3
SNTN
ZKSCAN7
ZNF502
QRICH1
FAM3D
MIR425
MIRLET7G
U3\|ENSG00000200222.1
RNA5SP133
RN7SKP45
RNA5SP130
RNA5SP132
U3\|ENSG00000202268.1
RNA5SP131
PRSS50
SNORD38\|ENSG00000207109.1
MIR191
MIR564
MIR566
MIR135A1
RNU6ATAC26P
SACM1L
MIR711
U3\|ENSG00000212211.1
SNORD69
SNORD19\|ENSG00000212493.1
SNORA26\|ENSG00000212608.1
TMEM110
NCKIPSD
TREX1
IQCF5
IQCF6
IFRD2
RNU6ATAC29P
MIR1284
RNU6ATAC16P
MIR1226
MIR1324
ARIH2OS
SNORD19\|ENSG00000222345.1
RN7SKP61
RNA5SP136
SLC26A6
LINC00694
PRSS44
ZNF717
SPINK8
IQCF3
TMA7
GPX1
C3orf84
snoU13\|ENSG00000238350.1
snoU13\|ENSG00000238416.1
snoU13\|ENSG00000238565.1
snoU13\|ENSG00000238568.1
SNORD19B\|ENSG00000238862.1
snoU13\|ENSG00000238905.1
snoU13\|ENSG00000239128.1
RN7SL271P
ASB14
TLR9
RN7SL751P
LINC00877
TDGF1
RN7SL182P
RN7SL482P
RN7SL418P
RN7SL504P
LINC00960
RN7SL294P
LINC00870
NAT6
MUSTN1
RN7SL647P
ACY1
FAM86DP
LINC00698
RN7SL145P
RN7SL863P
RN7SL870P
TWF2
ABHD14A
TMEM158
snoU13\|ENSG00000251938.1
SNORD77\|ENSG00000251967.1
SNORD63\|ENSG00000251987.1
RNA5SP134
MIR2115
SNORD19B\|ENSG00000252787.1
RNA5SP135
RPP14
EBLN2
LINC00696
PRSS46
RN7SL821P
MIR5193
MIR4793
MIR3938
MIR4271
RN7SL217P
RN7SL321P
RN7SL664P
MIR3923
MIR3136
MIR4443
RN7SL92P
ESRG
MIR4273
LUZPP1
NPCDR1
MIR4787

Genes in Wide Peak

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

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

Genes
FSTL3
TCF3
STK11
PTBP1
CNN2
ABCA7
SBNO2
WDR18
FGF22
RNF126
DAZAP1
MBD3
REXO1
EFNA2
CIRBP
ATP5D
C19orf26
CDC34
MISP
POLR2E
POLRMT
HCN2
PALM
MADCAM1
THEG
MIER2
REEP6
PCSK4
APC2
RPS15
NDUFS7
KISS1R
ARID3A
GRIN3B
C19orf25
UQCR11
KLF16
SHC2
LPPR3
ABHD17A
GAMT
ATP8B3
CSNK1G2
TPGS1
PPAP2C
MUM1
GPX4
MIDN
AZU1
BSG
MED16
OR4F17
HMHA1
MEX3D
ODF3L2
TMEM259
C2CD4C
PRSS57
ADAMTSL5
PLK5
PRTN3
GZMM
ELANE
CFD
R3HDM4
ONECUT3
ADAT3
MIR1909
WASH5P
SCAMP4
C19orf24
FAM138F
RN7SL477P
RNA5SP462
MIR3187
MIR4745
RN7SL226P
UQCR11

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.11.

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

Genes
HUNK
SOD1
TIAM1
SCAF4
SNORA81\|ENSG00000238390.1
MIR4327

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q13.3.

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

Genes
PIK3R1
DEPDC1B
VCAN
ZFYVE16
ERCC8
ADAMTS6
HEXB
PTCD2
RIOK2
KIF2A
MAST4
MEF2C
TNPO1
TAF9
SCAMP1
DIMT1
IPO11
ERBB2IP
NUDT12
MRPS27
HMGCR
COL4A3BP
PDE8B
ARSB
THBS4
MSH3
RASGRF2
POLR3G
ARRDC3
FAM172A
LNPEP
ST8SIA4
PPWD1
TRIM23
TRAPPC13
ELL2
POLK
SV2C
NLN
CENPK
COX7C
ZSWIM6
MAP1B
CKMT2
ZCCHC9
MCCC2
DMGDH
BHMT2
AP3B1
ZBED3
ANKRD32
MRPS36
CCNB1
CDK7
CD180
CCNH
FAM159B
HAPLN1
LHFPL2
SSBP2
BHMT
ANKRD31
IQGAP2
CRHBP
RASA1
LIX1
GIN1
PPIP5K2
PAM
BDP1
GTF2H2
SLC30A5
BTF3
FBXL17
SPATA9
ATG10
POC5
FAM151B
JMY
HOMER1
XRCC4
PART1
MARVELD2
RAD17
SREK1IP1
CWC27
CENPH
CAST
CETN3
FAM81B
SREK1
CHD1
FCHO2
TMEM171
EDIL3
TMEM161B
ELOVL7
NDUFAF2
RNF180
GPR98
F2RL2
F2RL1
AGGF1
WDR41
ARSK
RHOBTB3
SPZ1
SERINC5
ERAP1
ERAP2
CMYA5
TMEM174
CARTPT
PAPD4
ANKRA2
UTP15
NSA2
GFM2
PMCHL2
TBCA
OTP
ENC1
S100Z
SERF1A
SMN1
ACOT12
GLRX
SLCO4C1
FAM174A
RGMB
TMEM167A
PCSK1
RFESD
MCTP1
NR2F1
LYSMD3
MBLAC2
GCNT4
MTX3
GPR150
ZNF366
HTR1A
C5orf64
F2R
C5orf30
CCDC125
GTF2H2C
EFNA5
KIAA0825
LRRC70
RPS23
RGS7BP
SMIM15
ANKDD1B
ANKRD34B
OCLN
SGTB
TTC37
FAM169A
MIR3607
RNA5SP188
RNA5SP189
RNY3P1
SLCO6A1
NBPF22P
ATP6AP1L
SMN2
SERF1B
SNORA18\|ENSG00000206592.1
SNORA70\|ENSG00000206958.1
RNA5SP187
RN7SKP62
MIR583
U8\|ENSG00000212249.2
SNORA40\|ENSG00000212363.1
ARHGEF28
SNORA50\|ENSG00000220986.1
MIR548P
RN7SKP68
FKSG52
GTF2H2B
DHFR
C5orf27
snoU13\|ENSG00000238334.1
snoU13\|ENSG00000238400.1
snoU13\|ENSG00000238451.1
snoU13\|ENSG00000238688.1
snoU13\|ENSG00000238740.1
SCARNA18\|ENSG00000238835.1
SNORA47
snoU13\|ENSG00000239159.1
RN7SL782P
RN7SL255P
RN7SL629P
RN7SL169P
RN7SL814P
RN7SL153P
LINC00461
LUCAT1
POU5F2
7SK\|ENSG00000249352.3
NAIP
LINC00491
LINC00492
FOXD1
MIR2277
RN7SKP122
SNORA31\|ENSG00000251828.1
RN7SKP34
RN7SKP157
SNORA31\|ENSG00000252337.1
RNU6ATAC36P
RNA5SP186
SNORA76\|ENSG00000252904.1
RN7SKP295
GUSBP3
MIR4804
RN7SL476P
MIR4803
RN7SL802P
MIR3660
RN7SL208P
RN7SL9P
RN7SL378P
MIR4280
RN7SL103P
RN7SL616P
CKS1B\|ENSG00000268942.1
MTRNR2L2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q24.32.

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

Genes
NT5C2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q14.12.

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

Genes
NUFIP1
TSC22D1
TPT1
KIAA1704
COG3
FAM194B
SLC25A30
KCTD4
GTF2F2
SNORA31\|ENSG00000199477.1
RNA5SP27
RN7SKP3
LINC00330
snoU13\|ENSG00000238932.1
SNORA31\|ENSG00000253051.1
RN7SL49P
7SK\|ENSG00000271818.1

Genes in Wide Peak

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

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

Genes
CUL2
PARD3
LINC00838
MIR3611

Genes in Wide Peak

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

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

Genes
PSME4
GPR75
snoU13\|ENSG00000238756.1
MIR3682

Genes in Wide Peak

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

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

Genes
NCF1
GTF2IRD2

Genes in Wide Peak

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

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

Genes
PSPC1
ZMYM5
TPTE2
MPHOSPH8
TUBA3C
LINC00350
PHF2P2
LINC00388
LINC00349
LINC00387
LINC00442
LINC00421
snoU13\|ENSG00000238665.1
RNA5SP24
RN7SL166P

Genes in Wide Peak

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

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

Genes
BCL7A
ALDH2
PTPN11
CRY1
NR1H4
POLR3B
IGF1
RNF10
ZCCHC8
MPHOSPH9
RIMBP2
SFSWAP
CHFR
SCARB1
NUAK1
WSCD2
ACTR6
NUP37
SLC25A3
SART3
UNG
ANKRD13A
ACACB
AACS
SSH1
TMED2
DYNLL1
TESC
RPL6
MAPKAPK5
P2RX7
ANAPC5
SLC24A6
KDM2B
LHX5
OAS1
GCN1L1
RPLP0
PXN
SIRT4
RPH3A
PEBP1
TBX5
BRAP
ERP29
NOS1
ZNF268
GOLGA3
PITPNM2
PSMD9
PRDM4
COQ5
SELPLG
CORO1C
DAO
KCTD10
MLEC
MVK
CAMKK2
RSRC2
TRPV4
ARPC3
GPN3
VPS29
MYL2
CUX2
SH2B3
ACAD10
NAA25
OGFOD2
CDK2AP1
OAS3
OAS2
RASAL1
GTF2H3
EIF2B1
DDX55
C12orf49
FZD10
RFC5
STX2
GPR133
UHRF1BP1L
CHPT1
GNPTAB
NT5DC3
SUDS3
PRKAB1
HCFC2
RAB35
COX6A1
RFX4
RIC8B
SRSF9
FBRSL1
CCDC92
UTP20
TMPO
ARL1
GLT8D2
MTERFD3
NFYB
CCDC53
APAF1
RBM19
CIT
IFT81
ACADS
HVCN1
DDX54
MED13L
PIWIL1
CLIP1
CCDC62
HIP1R
C12orf65
RAN
TAOK3
USP30
SDS
MSI1
HNF1A
FBXO21
TBX3
OASL
HRK
RNFT2
P2RX4
CCDC64
DTX1
TRAFD1
ISCU
ALDH1L2
STAB2
SCYL2
CKAP4
APPL2
PWP1
DRAM1
KIAA1033
SLC41A2
SYCP3
ASCL1
GAS2L3
TMEM132B
SLC15A4
TDG
C12orf52
SDSL
MMAB
GLTP
GIT2
TCHP
FAM222A
FOXN4
SBNO1
MORN3
SETD1B
VPS33A
VPS37B
RHOF
DENR
SRRM4
ABCB9
RILPL2
DHX37
UBC
C12orf45
C12orf23
BTBD11
UBE3B
RAD9B
PLBD2
ANO4
GLT1D1
TMEM132D
HSPB8
CABP1
SPPL3
C12orf43
WDR66
HPD
LRRC43
TCP11L2
SVOP
IKBIP
DEPDC4
SPIC
IQCD
HSP90B1
POP5
TCTN2
RNF34
TRIAP1
PLA2G1B
CHST11
KSR2
MAP1LC3B2
PAH
HECTD4
CCDC63
ATP2A2
C12orf76
MYO1H
CMKLR1
FBXW8
MLXIP
UNC119B
B3GNT4
VSIG10
WSB2
PXMP2
ANKLE2
POLE
ULK1
PUS1
FAM101A
C12orf42
ZNF664
SLC17A8
FAM71C
TMEM132C
ARL6IP4
ORAI1
HCAR2
GALNT9
TMEM119
CCDC60
PMCH
EP400
SETD8
DIABLO
SNRNP35
KNTC1
NOC4L
BRI3BP
ANKS1B
DDX51
ATP6V0A2
PARPBP
EP400NL
PPP1CC
CCDC42B
TPCN1
P2RX2
ASCL4
RILPL1
TMEM120B
ALKBH2
LINC00943
MYBPC1
ZNF140
ZNF605
NCOR2
ANAPC7
LINC00173
PPTC7
HCAR1
DNAH10
ZNF84
TMEM116
FAM109A
ZNF26
TXNRD1
MMP17
FICD
RNA5SP370
RNA5SP374
RNA5SP375
SNORD56\|ENSG00000200112.1
RNA5SP378
RN7SKP250
SNORD74\|ENSG00000200897.1
SNORA38\|ENSG00000201042.1
RNA5SP368
RN7SKP71
RNA5SP379
SNORA70\|ENSG00000201945.1
RNA5SP366
SNORD50\|ENSG00000202335.1
LRCOL1
IL31
ATXN2
TCTN1
FAM216A
C12orf73
SNORA9\|ENSG00000206897.1
MIR619
MIR620
SNORA49
RNA5SP372
RNA5SP377
RNA5SP376
SNORA53
U8\|ENSG00000212594.1
ZNF891
MIR1178
RNA5SP371
RN7SKP216
RNA5SP369
TMEM233
ANHX
ADAM1A
C12orf75
GOLGA2B
snoU13\|ENSG00000238748.1
snoU13\|ENSG00000238800.1
snoU13\|ENSG00000238822.1
snoU13\|ENSG00000238895.1
snoU13\|ENSG00000238914.1
snoU13\|ENSG00000238940.1
RPS27P25
RN7SL865P
RPL22P19
RN7SL441P
RN7SL508P
PGAM5
LINC00939
DNAH10OS
SNORA9\|ENSG00000252192.1
RNU4ATAC12P
RNA5SP367
SNORA27\|ENSG00000252459.1
RN7SKP197
RNA5SP373
EID3
HCAR3
LINC00944
LINC00507
ZNF10
SLC5A8
LINC00508
GATC
LINC00485
MIR4497
RN7SL387P
SNORA40\|ENSG00000264043.2
MIR3922
RN7SL179P
RN7SL793P
RN7SL769P
RN7SL534P
MIR4419B
MIR3652
MIR5188
MIR4700
MIR4304
RN7SL133P
MIR3612
MIR3657
RN7SL176P
MIR3908
MIR4498
MUC8
U7\|ENSG00000272215.1
snoU13\|ENSG00000272464.1

Genes in Wide Peak

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

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

Genes
RBM15
TRIM33
NRAS
ST7L
CSDE1
CLCA1
CLCA4
GCLM
SARS
SIKE1
COL11A1
DDX20
CHI3L2
GNAI3
PKN2
EVI5
DNTTIP2
TGFBR3
KIAA1107
CDC14A
RSBN1
MAGI3
WDR47
OVGP1
SLC25A24
SH3GLB1
CDC7
PALMD
STXBP3
KIAA1324
AMPD2
KCNC4
WDR77
ATP5F1
RAP1A
CAPZA1
AMPD1
BCAS2
OLFML3
PHTF1
CD58
CD2
GBP3
GBP1
TMED5
DR1
CNN3
F3
ABCD3
DPH5
PTBP2
LPPR5
LPPR4
SLC35A3
DCLRE1B
CASQ2
OLFM3
LRIF1
ADORA3
CLCC1
GPSM2
RPL5
ODF2L
TRMT13
LRRC39
RWDD3
ZNF644
CCDC18
RPAP2
GNAT2
GSTM1
PRPF38B
TSPAN2
TSHB
GSTM5
GSTM3
SYT6
VAV3
CHIA
PSRC1
PTPN22
SORT1
WNT2B
LAMTOR5
CEPT1
NGF
AP4B1
BCAR3
FNBP1L
CCBL2
GTF2B
BRDT
ARHGAP29
CLCA2
DBT
RTCA
LMO4
SYPL2
BARHL2
MTF2
SLC44A3
IGSF3
CTTNBP2NL
STRIP1
KCNA10
PSMA5
FNDC7
C1orf162
CD53
PROK1
CELSR2
TMEM56
CLCA3P
HS2ST1
GBP5
FAM69A
MOV10
RHOC
PPM1J
SLC16A1
GPR61
ALX3
DRAM2
FRRS1
HIAT1
SASS6
SNX7
NTNG1
FAM102B
HENMT1
AKNAD1
GBP2
ATXN7L2
GBP4
ZNF326
HFM1
GFI1
AGL
VCAM1
EXTL2
SLC30A7
DENND2D
HIPK1
SLC22A15
ATP1A1
SLC16A4
AHCYL1
GSTM4
S1PR1
KCND3
LRRC8C
LRRC8D
COL24A1
EPHX4
ALG14
MAB21L3
VANGL1
PIFO
CYB561D1
GLMN
AMY1B
DENND2C
KCNA3
KCNA2
NHLH2
C1orf194
GPR88
AMIGO1
GBP6
CSF1
FAM19A3
RNPC3
NBPF6
UBL4B
AMY1C
DPYD
BCL2L15
BTBD8
NBPF4
SLC6A17
LRRC8B
TAF13
FAM212B
ABCA4
EPS8L3
SYCP1
LRIG2
PRMT6
RNA5SP52
U3\|ENSG00000199666.1
SNORA25\|ENSG00000200536.1
RNA5SP51
C1orf137
ATP1A1OS
CHIAP2
SPATA42
C1orf146
SNORD21
RNU6V
SNORA51\|ENSG00000207022.1
SNORA42\|ENSG00000207502.1
SNORA66\|ENSG00000207523.1
MIR197
MIR553
MIR320B1
MIR760
RNA5SP53
GSTM2
GBP7
RBMXL1
TMEM167B
U3\|ENSG00000221040.1
MYBPHL
RN7SKP285
RN7SKP123
RN7SKP270
MIR137HG
GBP1P1
PGCP1
ACTBP12
AMY1A
snoU13\|ENSG00000238296.1
snoU13\|ENSG00000238389.1
snoU13\|ENSG00000238761.1
snoU13\|ENSG00000238975.1
snoU13\|ENSG00000239111.1
snoU13\|ENSG00000239176.1
RN7SL583P
RN7SL692P
RN7SL653P
RN7SL420P
AMY2B
CYMP
SLC25A24P1
RN7SL831P
RN7SL824P
RN7SL432P
AMY2A
NBPF5P
SNORA66\|ENSG00000251795.1
RNA5SP55
RNA5SP54
SCARNA16\|ENSG00000252765.1
RN7SKP272
MIR378G
MIR548AC
RN7SL440P
RN7SL235P
SCARNA2

Genes in Wide Peak

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

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

Genes
BCL3
FSTL3
TCF3
CIC
GNA11
ERCC2
LYL1
AKT2
CD79A
PPP2R1A
TFPT
JAK3
ELL
STK11
SMARCA4
MLLT1
ZNF331
BRD4
SH3GL1
CBLC
TPM4
KLK2
CEBPA
HSPB6
ARHGAP33
UPF1
SPPL2B
C19orf60
CRLF1
TBXA2R
LGALS14
PAF1
MARK4
CCDC124
CEACAM21
TRAPPC6A
MATK
CEACAM7
MPND
PGLYRP1
NFIX
GIPR
FUZ
APBA3
AKAP8L
PTBP1
DPF1
PLAUR
WIZ
QPCTL
PPP5C
ZBTB32
TYROBP
ERCC1
CD22
PSMC4
ZNF582
SLC7A9
NLRP2
EHD2
POU2F2
RANBP3
PNPLA6
UHRF1
MRI1
PNKP
BEST2
AP2S1
HOMER3
USE1
GNA15
CREB3L3
ZNF112
POLD1
SLC6A16
GLTSCR1
SPHK2
RPL18
CA11
ISOC2
U2AF2
EPN1
MED29
RFXANK
TMEM161A
LPAR2
SUGP2
CNN2
ABCA7
SBNO2
HMG20B
AP3D1
WDR18
TLE2
PDE4A
ELAVL1
SIRT2
FGF22
RNF126
DAZAP1
MBD3
PRKACA
LPHN1
TMEM38A
AP1M1
PVR
XRCC1
NOTCH3
TEAD2
C19orf10
ANO8
WDR62
GPATCH1
ICAM3
CAMSAP3
XAB2
ARHGEF1
STXBP2
MAP2K7
NMRK2
SNRPA
EXOSC5
SIRT6
REXO1
CEACAM1
LIPE
PAFAH1B3
DNM2
KEAP1
PTPRH
RDH8
COL5A3
ZNF506
SLC27A5
ZNF324
ZNF671
ZNF416
ZNF586
ZNF446
ZNF8
ZNF264
RPS5
CHERP
ITPKC
CEACAM6
MYBPC2
PPP1R15A
HSD17B14
FTL
BAX
RFX2
SULT2B1
CNOT3
GP6
KHSRP
FXYD5
ZNF302
GRAMD1A
FXYD3
GMIP
ANKRD24
LTBP4
BLVRB
ICAM1
STRN4
FLT3LG
CD209
CERS4
MCOLN1
FCGBP
PLEKHG2
DLL3
NAT14
OR1I1
DHPS
HOOK2
IL11
C19orf77
IL12RB1
TMED1
MAST3
MZF1
OCEL1
MYO9B
KCNK6
CATSPERG
PSMD8
EFNA2
CIRBP
ATP5D
C19orf26
HNRNPM
MARCH2
NDUFB7
TECR
TIMM13
CDC34
MISP
POLR2E
POLRMT
HCN2
IZUMO4
GADD45B
PALM
MADCAM1
MKNK2
ACP5
MAN2B1
KCNN4
TULP2
NUCB1
DHDH
GYS1
MAP4K1
CGB2
ECH1
HNRNPL
NFKBIB
LHB
CGB
TUBB4A
SARS2
KCNA7
SNRNP70
CLPTM1
RELB
CLASRP
LIN7B
PPP1R37
FCGRT
PIH1D1
CKM
ARHGEF18
PPP1R13L
PEX11G
DOT1L
PLEKHJ1
SLC17A7
RNASEH2A
KLC3
CD37
SF3A2
AMH
DKKL1
OAZ1
TRMT1
STX10
RETN
FCER2
DMPK
CLEC4M
RSPH6A
TBC1D17
IL4I1
TLE6
CCDC130
PTOV1
AES
NOVA2
SGTA
KIR3DX1
LILRB1
MED25
LILRA1
SNAPC2
C19orf53
TIMM44
CCDC61
IL27RA
ASF1B
TNNT1
VRK3
FAM32A
PPP6R1
C19orf44
MED26
OLFM2
RASAL3
AKAP8
EPHX3
ILVBL
ZNF419
SYDE1
CASP14
SLC1A6
AURKC
POP4
CCNE1
URI1
PDCD5
ANKRD27
RPS16
TIMM50
LGALS13
FBL
DYRK1B
CLC
CNTD2
GPI
PLD3
PRX
PIAS4
NUMBL
EBI3
CCDC94
SHD
TBCB
FSD1
POLR2I
OVOL3
CLIP3
ZFR2
SLC1A5
PRKD2
TJP3
APLP1
CACTIN
CCDC9
HNRNPUL1
FZR1
BBC3
TGFB1
ATP5SL
CEACAM4
PLIN3
MYH14
MRPL4
SIGLEC8
LIM2
ICAM4
RPS19
GLTSCR2
NKG7
ICAM5
ETFB
CD33
CEACAM5
CRX
BABAM1
TYK2
SULT2A1
CDC37
NAPA
RABAC1
ATP1A3
MEIS3
PTPRS
CNFN
ZNRF4
MEGF8
KDELR1
CYTH2
GRWD1
GRIN2D
SYNGR4
CLEC11A
CCDC114
CARD8
LIG1
SIGLEC6
ZNF175
PLA2G4C
SIGLEC5
CABP5
HAS1
RAB3D
DBP
TMEM205
CAPS
DKFZP761J1410
FAM83E
RASIP1
THEG
FGF21
BCAT2
MIER2
PLEKHA4
TNPO2
WDR83OS
CACNG7
GCDH
LILRB5
KLF1
DNASE2
MAST1
LENG1
PRPF31
RPL18A
SLC5A5
ARRDC2
PIK3R2
RAB3A
PDE4C
ISYNA1
CRTC1
KMT2B
COMP
UPK1A
COPE
DDX49
ETV2
ATP4A
ARMC6
TMEM147
GAPDHS
MAG
TMEM59L
HAMP
USF2
LSR
KXD1
FKBP8
SUGP1
HPN
ZNF14
SCN1B
PBX4
ERF
GSK3A
ATP13A1
ZNF574
GRIK5
SIPA1L3
ZNF85
ETHE1
CADM4
SMG9
UBE2S
RPL28
REEP6
PCSK4
APC2
RPS15
NDUFS7
KISS1R
ARID3A
GRIN3B
CD3EAP
ZNF541
SLC8A2
KPTN
ZNF430
C19orf25
ZBTB45
ZFP30
CEP89
TSHZ3
ZNF549
A1BG
ZSCAN18
ZNF211
DDX39A
PKN1
C19orf43
CD97
WDR83
GIPC1
B9D2
ADCK4
ZNF137P
PEPD
CHST8
HIF3A
ZNF576
IRGC
ZNF45
LYPD3
PSG8
CEACAM8
KIR2DL1
PPP1R12C
MBOAT7
SLC25A23
PSPN
GTF2F1
ALKBH7
CLPP
TNFSF9
CD70
C3
SH2D3A
TRIP10
GPR108
TNFSF14
FOSB
OPA3
SNRPD2
RTN2
EML2
VASP
SYMPK
S1PR4
NCLN
LRFN3
IGFLR1
CAPNS1
PDCD2L
GPR42
RBM42
KIRREL2
UBA2
FFAR2
HCST
FFAR1
COX6B1
BCL2L12
IRF3
PRMT1
RRAS
PRRG2
SCAF1
PRR12
TSKS
PRKCG
MAP2K2
ABHD8
PIN1
FBXL12
EMR2
SIN3B
OR7A10
SLC35E1
EPS15L1
KLF2
OR7C2
OR7C1
F2RL3
UQCR11
KDM4B
TICAM1
ZNF835
ZNF780B
LRFN1
ZFP36
MRPS12
KRI1
ILF3
SLC44A2
AP1M2
CDKN2D
KLK14
SIGLEC9
KLK10
KLK8
KLF16
DOHH
MAU2
SHC2
LPPR3
ABHD17A
SYT5
TNNI3
GAMT
DOCK6
ECSIT
LDLR
ELOF1
TSPAN16
C19orf80
PRKCSH
CNN1
EXOC3L2
PVRL2
APOE
TOMM40
APOC1
FAM98C
SAFB2
RPL36
ATP8B3
GDF1
NCAN
GTPBP3
PLVAP
BST2
SLC27A1
USHBP1
COLGALT1
DDA1
MRPL34
PGLS
LSM7
ACSBG2
FUT5
ACTN4
CACNG6
FCHO1
UNC13A
MAP1S
SSBP4
GDF15
PGPEP1
KIAA1683
LSM4
JUND
HRC
TRPM4
ZNF557
CRB3
CYP2G1P
PAK4
CHMP2A
UBE2M
TRIM28
YIPF2
ATG4D
TMEM160
ZC3H4
NPAS1
GMFG
MAP3K10
ZNF317
PPAN
EIF3G
ANGPTL6
C19orf66
DNMT1
ZNF426
SLC7A10
LRP3
EPS8L1
LILRB2
ZNF227
ZNF428
TEX101
CCL25
HAUS8
EMR3
KCNC3
NAPSA
NAPSB
NR1H2
LRRC4B
ZNF304
ZSCAN5A
ZNF132
USP29
RHPN2
C19orf12
C19orf40
PODNL1
DNAJB1
ZSWIM4
FBXW9
RFX1
ZNF20
C19orf57
DCAF15
CC2D1A
RTBDN
BTBD2
PRAM1
SUV420H2
ZNF414
HSPBP1
CSNK1G2
DHX34
C5AR2
CACNA1A
SAMD1
SLC39A3
NFIC
TPGS1
PPAP2C
ZIM3
FEM1A
VAV1
MVB12A
CIB3
DUS3L
DPP9
DMRTC2
CCDC97
TMEM91
ZFP14
EMP3
SAE1
NTN5
LMTK3
GEMIN7
WTIP
ADAMTS10
MYO1F
NLRP12
CACNG8
ZNF787
C19orf52
FBN3
CARM1
EVI5L
GPR32
SIGLEC10
ACPT
KLK3
ZNF473
FAM71E1
RPS11
PTH2
SPIB
RPL13A
CTU1
NOSIP
IGLON5
RCN3
ZNF614
ZNF547
ZNF773
ZNF776
ZNF256
ZSCAN1
ZNF837
CEBPG
KCTD15
ZNF599
LGI4
FUT6
LYPD5
ZNF230
ZNF222
ZNF221
ZNF233
ZNF235
ARHGAP35
PTGIR
CALM3
CPAMD8
NR2F6
ANKLE1
CILP2
ZNF66
CLDND2
ZNF208
ZNF761
ZNF714
C19orf47
HIPK4
SHKBP1
RDH13
SPTBN4
BRSK1
COX6B2
TMEM190
NLRP4
DEDD2
SAFB
NACC1
IER2
PTGER1
MUM1
ZNF333
CCDC105
PGLYRP2
CELF5
MFSD12
FBXO27
DMKN
U2AF1L4
NPHS1
THAP8
COX7A1
ZNF382
ZNF577
TMEM143
CCDC155
ALDH16A1
SIGLEC11
SIGLEC16
IZUMO2
EMC10
JOSD2
SHANK1
OR7G1
RAVER1
SYCE2
SPC24
ZNF653
BIRC8
PLEKHF1
WDR88
KIAA0355
ZNF606
ZNF91
IRGQ
ZNF226
ZNF229
ZNF180
GNG8
LINC00905
RAB8A
GPX4
MIDN
JSRP1
FAM129C
KLHL26
GATAD2A
ZNF610
ZNF528
ZNF701
SERTAD3
RAB4B
C19orf55
CYP2S1
AXL
NFKBID
TMC4
LAIR1
TTYH1
LENG8
CDC42EP5
LAIR2
TMEM145
ZNF526
KIR3DL1
NLRP7
ZNF146
ZNF283
PPP1R14A
SPINT2
C19orf33
YIF1B
DNAAF3
ATCAY
DAPK3
EEF2
TMIGD2
CHAF1A
UBXN6
HDGFRP2
PLIN4
SEMA6B
ZNF444
HSD11B1L
C19orf48
KLK1
KLK4
KLK5
KLK6
KLK11
KLK13
ZNF83
ACER1
ANGPTL4
NDUFA7
CD320
ZNF558
C3P1
PRDX2
ZNF30
ZNF507
SIGLEC7
UQCRFS1
KLK7
ATF5
CPT1C
ELSPBP1
CCDC8
IRF2BP1
FOXA3
ZNF296
PSG6
LILRA3
RPS9
TSEN34
NDUFA3
OSCAR
OR7G3
OR7G2
OR1M1
MBD3L1
ZNF160
ZNF415
CEACAM3
LRRC8E
FPR2
FPR1
SIGLEC17P
INSR
NRTN
FUT3
RLN3
JUNB
LRG1
ZNF439
ZNF440
ZNF581
ZNF524
ZNF562
ZNF561
NLRP5
ZNF584
ZNF274
ZIK1
LGALS4
NXNL1
RASGRP4
WDR87
ZNF540
ZNF570
CYP4F11
OR10H3
OR10H2
CYP4F22
ZNF57
ZNF556
ZNF554
THOP1
MOB3A
AZU1
BSG
OR10H5
ZNF738
ZNF417
NLRP13
CCDC106
TDRD12
ZNF791
SWSAP1
RAX2
TTC9B
KLK15
ZNF497
ZNF266
OR7D4
PCP2
EMR1
NDUFA11
CATSPERD
C19orf70
FUT1
MED16
LRRC25
ZNF77
ZNF613
MYPOP
ZNF404
OR10H4
ZNF135
CEACAM20
EID2
EID2B
ZNF575
DIRAS1
PHLDB3
GNG7
LMNB2
OR4F17
MAMSTR
FUT2
C19orf18
SIX5
FBXO46
B3GNT8
SPACA4
PPFIA3
GPR4
FAM187B
ZNF491
STAP2
TSSK6
ZNF114
VN1R1
ZNF543
TMPRSS9
ZNF223
CTXN1
DPY19L3
TPRX1
LGALS7B
ZNF552
ZBTB7A
SEPW1
EIF3K
FARSA
SAMD4B
GGN
SIGLECL1
CALR
RAD23A
GADD45GIP1
DAND5
NLRP8
SYCN
MYADM
NKPD1
GIPC3
NLRP11
ZNF154
B3GNT3
ZNF784
FIZ1
SSC5D
FAM71E2
TMEM150B
TMEM86B
ZNF816
HMHA1
ZNF571
ZSCAN4
S1PR5
ZNF443
ZNF792
ZFP82
FKRP
TRAPPC5
SLC25A42
MUC16
SLC25A41
SYNE4
MEX3D
HKR1
OR2Z1
ODF3L2
ACTL9
ZNF329
ZNF101
PNMAL1
TMEM259
ZNF708
IZUMO1
LINC00085
MBD3L3
ZSCAN22
KCNJ14
IFNL1
CAPN12
CLEC4G
LENG9
ZNF320
C19orf59
LYPD4
C2CD4C
RUVBL2
C19orf71
CCDC159
MRPL54
ZNF530
PSG9
IFNL2
PAPL
ZNF730
NR2C2AP
ZNF93
PRSS57
RAB11B
TNFAIP8L1
OR7A17
C19orf68
ADAMTSL5
NLRP9
DMWD
ZNF829
FFAR3
PLK5
NDUFA13
ZNF566
ZNF529
ZNF284
PIP5K1C
CYP4F2
CYP4F12
ZNF749
ZNF17
ZNF555
RGS9BP
FCAR
KLK12
CYP4F8
CYP4F3
CEACAM19
OR10H1
VSIG10L
LILRB4
SELV
KANK3
LILRA5
VSTM2B
ZNF546
BCAM
EPOR
FPR3
SBK2
NANOS3
VMAC
HAPLN4
PALM3
SHISA7
CLEC17A
RINL
OR7D2
C19orf67
ZNF490
NWD1
TMEM221
ZNF626
ZNF793
OR7A5
ZNF383
IGFL1
C19orf35
ZNF559
BSPH1
PRR19
NANOS2
ZNF788
C19orf54
NCCRP1
KRTDAP
IGFL3
ZNF177
SPRED3
ZNF548
ZNF563
SBSN
KIR2DL4
ZNF567
CGB5
VSTM1
BLOC1S3
ZNF573
ZNF527
ZNF600
FAM90A27P
CXCL17
NCR1
ZNF724P
ZNF676
ZNF699
VN1R2
ZNF681
ZNF766
RYR1
SUPT5H
ZNF471
ZNF836
ZNF493
CGB7
ZNF729
ZNF565
ELAVL3
LONP1
ZNF781
PRTN3
ZNF765
ZNF569
ZNF799
ZNF846
ZNF136
HSH2D
ZNF431
ZNF418
ZNF700
ZNF709
ZFP28
AP2A1
ZNF585A
ZNF429
ZNF470
SERTAD1
ZNF100
ZNF441
ZNF420
ZNF763
IFNL3
ZNF682
ZNF772
ZNF257
ZSCAN5B
KANK2
ZNF833P
ZNF98
ZNF675
DACT3
C5AR1
CYP2B6
CYP2F1
ZNF628
GALP
ZNF665
GZMM
ELANE
KLKP1
ZNF841
ZNF615
ZNF433
ZNF460
CFD
ZNF780A
ZNF461
CYP2A13
ZNF181
ZNF44
ZNF790
ZNF677
ZNF823
ZNF347
ZNF71
ZNF121
CCDC151
ZNF560
ZNF667
CYP2A7
ZNF649
ZNF544
ZNF607
UBL5
PEG3
ZNF442
ZNF813
ASNA1
ZNF69
ZNF583
ZNF568
ZNF480
ZNF587
ZNF808
ZNF43
ZNF28
ZNF627
ZNF536
ZNF534
C19orf45
ZNF358
R3HDM4
MIRLET7E
MIR371A
MIR330
MIR372
MIR373
SNORD33\|ENSG00000199631.1
RNA5SP463
SNORA70\|ENSG00000200237.1
SNORD35A
SNORD35B
RNA5SP472
RNA5SP469
SNORA68\|ENSG00000201388.1
SNORD32A
RN7SKP22
SNORD34
ZNF525
ZNF814
ZNF551
ZNF805
ZSCAN5C
LILRB3
DPRX
ZNF468
ZNF616
ASPDH
AKT1S1
PNMAL2
IGFL2
IGFL4
ZNF155
CD177
PSG5
C19orf69
LGALS7
SDHAF1
PSENEN
SCGB2B2
RPSAP58
LINC00661
RGL3
MBD3L4
DENND1C
ARRDC5
ONECUT3
SNORD37\|ENSG00000206775.1
SNORA68\|ENSG00000207166.1
MIR99B
MIR518C
MIR520F
MIR526B
MIR181D
MIR520A
MIR520E
MIR181C
MIR516A2
MIR526A1
MIR641
MIR518A2
MIR518F
MIR639
MIR525
MIR520B
MIR637
MIR517A
MIR520D
MIR520C
MIR518D
MIR199A1
MIR516A1
MIR642A
MIR150
MIR519C
MIR520G
MIR518A1
MIR522
MIR27A
MIR519E
MIR640
MIR519B
MIR517B
MIR517C
MIR520H
MIR518B
MIR498
MIR516B2
MIR516B1
MIR638
MIR524
MIR527
MIR23A
MIR519D
MIR518E
MIR519A1
MIR643
MIR125A
MIR523
SNORD105
SNORD41\|ENSG00000209702.1
MIR320E
MIR526A2
MIR769
PRR22
RNA5SP465
RNA5SP467
ZNF580
ZNF611
KLK9
SYT3
NUP62
CGB8
ZNF254
QTRT1
ADAT3
RPL23AP79
ZNF134
ZNF888
ZNF845
CEACAM18
PPM1N
CEACAM16
LEUTX
NUDT19
ZNF726
ZNF99
ZNF90
TM6SF2
MEF2B
SMIM7
UCA1
ZNF788
C19orf38
PLIN5
APOC1P1
MIR935
IFI30
IGSF23
ZNF579
LINGO3
ZGLP1
SNORD88C
MIR1323
U3\|ENSG00000221125.1
SNORD88A
SNORD88B
MIR1238
MIR1227
MIR1181
SNORD23\|ENSG00000221803.1
PSG3
ZNF321P
PSG7
C19orf73
ZNF880
FXYD7
KIR2DS4
UBA52
RN7SKP109
MIR1909
ZNF844
TINCR
RFPL4A
CERS1
ADM5
ZNF812
WASH5P
NTF4
OR7E19P
LGALS17A
SRRM5
SCAMP4
C19orf24
VN1R4
RFPL4AL1
ZNF492
PET100
PPP5D1
MBD3L2
CEACAM22P
ZNF826P
SGK110
PSG1
LINC00665
SEC1P
TMEM238
FAM138F
RPS28
PINLYP
APOC2
C19orf81
MBD3L5
ZNF737
OR7E24
snoU13\|ENSG00000238349.1
snoU13\|ENSG00000238486.1
snoU13\|ENSG00000238514.1
SNORD105B
snoU13\|ENSG00000238630.1
snoU13\|ENSG00000238838.1
snoU13\|ENSG00000239137.1
RN7SL477P
ALKBH6
CEACAMP3
RN7SL513P
RN7SL34P
RN7SL368P
LILRA4
LILRA2
RN7SL146P
ZNF542
KIR3DL2
RN7SL150P
RN7SL860P
RN7SL231P
TPM3P9
CEACAMP10
RN7SL70P
RN7SL836P
RN7SL340P
RN7SL566P
KIR3DL3
PSG2
RN7SL789P
RN7SL317P
ZNF702P
ZNF709
RN7SL842P
PSG11
PSG4
RN7SL337P
RN7SL364P
RN7SL526P
RN7SL844P
KIR2DL3
RN7SL402P
RN7SL833P
P2RY11
LILRA6
ZNF585B
BCKDHA
INSL3
PSG10P
TARM1
HAUS5
ZNF324B
ZNF564
LGALS16
YJEFN3
PRODH2
ZNF345
ZNF550
snoU13\|ENSG00000251709.1
RNA5SP464
snoU13\|ENSG00000252071.1
snoZ6\|ENSG00000252200.1
RNA5SP473
SNORD111\|ENSG00000252230.1
RNA5SP470
SNORD112\|ENSG00000252356.1
SNORD38\|ENSG00000252408.1
RNA5SP462
RNA5SP466
RNA5SP468
U3\|ENSG00000252683.1
RNA5SP471
SNORA70\|ENSG00000253027.1
ZNF260
SIGLEC14
SIGLEC12
MPV17L2
MEF2BNB
CYP2A6
TRAPPC2P1
ZNF432
ZNF486
ZNF225
CYP2B7P1
ZNF350
ZNF253
LSM14A
ZNF878
ZNF625
PRR24
ZNF578
DUXA
TPRX2P
TGFBR3L
ZNF865
LINC00662
MIA
ZNF234
MIR5196
MIR4747
MIR3187
MIR4750
RN7SL155P
RN7SL94P
RN7SL533P
RN7SL823P
MIR5684
RN7SL121P
RN7SL866P
RN7SL115P
MIR3189
RN7SL324P
RN7SL835P
MIR4322
RN7SL287P
RN7SL322P
RN7SL154P
RN7SL491P
RN7SL528P
MIR5088
RN7SL718P
MIR4752
RN7SL345P
RN7SL525P
MIR3191
RN7SL669P
RN7SL693P
MIR4999
MIR4324
MIR4751
RN7SL708P
RN7SL298P
MIR4745
RN7SL53P
MIR4748
RN7SL226P
MIR4749
RN7SL758P
MIR5589
RN7SL84P
MIR4323
RN7SL192P
RN7SL663P
MIR4746
RN7SL765P
MIR4530
RN7SL202P
MIR4754
RN7SL626P
MIR5695
MIR3940
RN7SL619P
LINC00663
FXYD1
MIR4321
ZNF223
ZNF850
UQCR11
C19orf82
ZNF763
LINC00906
APOC4
ZNF285
S1PR2
CYP4F24P
CGB1
FDX1L
ZNF224
LIN37
NDUFA7
CEA
ZSCAN5D
MIR3188
PIK3R2
SMIM17
SIGLEC5
MIMT1
LINC00664
SCGB1B2P
EMR4P
SIGLEC22P
CALR3
ZNF728
FAM90A28P
FBXO17
HCCAT3
ZNF587B
SPIB
CYP4F23P
ZIM2
KLK9
MIR1470
MIR519A2
EGLN2
MIR371B
ZNF177
LINC00904
THEG5
WBP7
IFNL4

Arm-level results

Table 3. Get Full Table Arm-level significance table - 19 significant results found. The significance cutoff is at Q value=0.25.

Arm	# Genes	Amp Frequency	Amp Frequency Score	Amp Z score	Amp Q value	Del Frequency	Del Frequency Score	Del Z score	Del Q value
1p	1300	0.14	0.19	0.423	0.937	0.22	0.26	2.19	0.0625
1q	1195	0.56	0.58	10.1	0	0.04	0.10	-1.19	1
2p	624	0.09	0.11	-1.74	0.999	0.20	0.22	0.633	0.57
2q	967	0.06	0.07	-2.43	0.999	0.20	0.21	0.782	0.529
3p	644	0.19	0.22	0.6	0.823	0.13	0.16	-0.583	1
3q	733	0.24	0.27	1.86	0.135	0.09	0.12	-1.48	1
4p	289	0.07	0.09	-2.38	0.999	0.24	0.26	1.31	0.282
4q	670	0.04	0.06	-2.8	0.999	0.23	0.24	1.27	0.282
5p	183	0.22	0.24	0.612	0.823	0.06	0.07	-2.82	1
5q	905	0.17	0.18	-0.0193	0.999	0.08	0.09	-1.98	1
6p	710	0.10	0.11	-1.79	0.999	0.10	0.11	-1.79	1
6q	556	0.09	0.11	-1.88	0.999	0.18	0.20	0.0144	0.868
7p	389	0.27	0.30	2.15	0.0772	0.10	0.14	-1.3	1
7q	783	0.24	0.26	1.79	0.144	0.07	0.09	-2.07	1
8p	338	0.32	0.40	4.14	0.000171	0.19	0.28	1.48	0.247
8q	551	0.40	0.43	5.5	2.46e-07	0.08	0.13	-1.21	1
9p	301	0.04	0.06	-2.77	0.999	0.30	0.31	2.53	0.0277
9q	700	0.04	0.06	-2.78	0.999	0.23	0.24	1.3	0.282
10p	253	0.11	0.14	-1.5	0.999	0.18	0.20	-0.127	0.868
10q	738	0.07	0.08	-2.35	0.999	0.18	0.19	0.0643	0.868
11p	509	0.08	0.09	-2.2	0.999	0.18	0.19	-0.0795	0.868
11q	975	0.04	0.05	-2.77	0.999	0.19	0.20	0.453	0.66
12p	339	0.12	0.14	-1.3	0.999	0.14	0.16	-0.84	1
12q	904	0.13	0.15	-0.635	0.999	0.13	0.15	-0.635	1
13q	560	0.06	0.09	-1.94	0.999	0.39	0.41	5.07	1.98e-06
14q	938	0.09	0.11	-1.57	0.999	0.19	0.21	0.636	0.57
15q	810	0.04	0.06	-2.64	0.999	0.26	0.27	1.97	0.0959
16p	559	0.40	0.47	6.06	1.35e-08	0.14	0.24	0.861	0.506
16q	455	0.20	0.37	2.97	0.00832	0.46	0.57	7.9	5.63e-14
17p	415	0.08	0.15	-0.871	0.999	0.48	0.52	7.25	3.94e-12
17q	972	0.18	0.25	1.48	0.246	0.29	0.35	3.87	0.00036
18p	104	0.12	0.18	-0.53	0.999	0.33	0.38	3.67	0.00068
18q	275	0.11	0.17	-0.674	0.999	0.34	0.39	4.05	0.000204
19p	681	0.03	0.04	-3.28	0.999	0.18	0.18	-0.141	0.868
19q	935	0.04	0.05	-2.79	0.999	0.19	0.20	0.416	0.66
20p	234	0.37	0.37	3.76	0.000563	0.00	0.00	-3.85	1
20q	448	0.37	0.37	4	0.000247	0.00	0.00	-3.76	1
21q	258	0.08	0.09	-2.53	0.999	0.13	0.14	-1.37	1
22q	564	0.04	0.08	-2.14	0.999	0.42	0.44	5.81	4.16e-08

Methods & Data

Input

Description

Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).
Markers File: The markers file identifies the marker names and positions of the markers in the original dataset (before segmentation). It is a three column, tab-delimited file with an optional header. The column headers are: (1) Marker Name, (2) Chromosome, (3) Marker Position (in bases).
Reference Genome: The reference genome file contains information about the location of genes and cytobands on a given build of the genome. Reference genome files are created in Matlab and are not viewable with a text editor.
CNV Files: There are two options for the cnv file. The first option allows CNVs to be identified by marker name. The second option allows the CNVs to be identified by genomic location. Option #1: A two column, tab-delimited file with an optional header row. The marker names given in this file must match the marker names given in the markers file. The CNV identifiers are for user use and can be arbitrary. The column headers are: (1) Marker Name, (2) CNV Identifier. Option #2: A 6 column, tab-delimited file with an optional header row. The 'CNV Identifier' is for user use and can be arbitrary. 'Narrow Region Start' and 'Narrow Region End' are also not used. The column headers are: (1) CNV Identifier, (2) Chromosome, (3) Narrow Region Start, (4) Narrow Region End, (5) Wide Region Start, (6) Wide Region End
Amplification Threshold: Threshold for copy number amplifications. Regions with a log2 ratio above this value are considered amplified.
Deletion Threshold: Threshold for copy number deletions. Regions with a log2 ratio below the negative of this value are considered deletions.
Cap Values: Minimum and maximum cap values on analyzed data. Regions with a log2 ratio greater than the cap are set to the cap value; regions with a log2 ratio less than -cap value are set to -cap. Values must be positive.
Broad Length Cutoff: Threshold used to distinguish broad from focal events, given in units of fraction of chromosome arm.
Remove X-Chromosome: Flag indicating whether to remove data from the X-chromosome before analysis. Allowed values= {1,0} (1: Remove X-Chromosome, 0: Do not remove X-Chromosome.
Confidence Level: Confidence level used to calculate the region containing a driver.
Join Segment Size: Smallest number of markers to allow in segments from the segmented data. Segments that contain fewer than this number of markers are joined to the neighboring segment that is closest in copy number.
Arm Level Peel Off: Flag set to enable arm-level peel-off of events during peak definition. The arm-level peel-off enhancement to the arbitrated peel-off method assigns all events in the same chromosome arm of the same sample to a single peak. It is useful when peaks are split by noise or chromothripsis. Allowed values= {1,0} (1: Use arm level peel off, 0: Use normal arbitrated peel-off).
Maximum Sample Segments: Maximum number of segments allowed for a sample in the input data. Samples with more segments than this threshold are excluded from the analysis.
Gene GISTIC: When enabled (value = 1), this option causes GISTIC to analyze deletions using genes instead of array markers to locate the lesion. In this mode, the copy number assigned to a gene is the lowest copy number among the markers that represent the gene.

Values

List of inputs used for this run of GISTIC2. All files listed should be included in the archived results.

Segmentation File = /cromwell_root/fc-c2229cb1-d1d1-425b-be11-72503bb3604d/f03723f0-d405-4150-a79d-05f949df49c0/aggregate_data_workflow/7bf32d97-3ae5-473a-88c8-083dc03295e4/call-aggregate_data/CPTAC3-BRCA-nonBasalTNBC.CNV__wxs.seg.txt
Markers File = ./this_file_does_not_exist.txt
Reference Genome = /cromwell_root/broad-institute-gdac/gdc/reference/gistic/hg19_GENCODE_v18_20140127.mat
CNV Files = /cromwell_root/broad-institute-gdac/gdc/reference/gistic/SNP6.merged.151117.hg19.CNV.txt
Amplification Threshold = 0.1
Deletion Threshold = 0.1
Cap Values = 1.5
Broad Length Cutoff = 0.98
Remove X-Chromosome = 0
Confidence Level = 0.99
Join Segment Size = 4
Arm Level Peel Off = 1
Maximum Sample Segments = 2000
Gene GISTIC = 1

Table 4. Get Full Table First 10 out of 90 Input Tumor Samples.

Tumor Sample Names
01BR015_TP
01BR017_TP
01BR023_TP
01BR025_TP
01BR030_TP
01BR032_TP
01BR033_TP
03BR002_TP
03BR004_TP
03BR005_TP

Figure 3. Segmented copy number profiles in the input data

Output

All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level)

The all lesions file summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

Region Data

Columns 1-9 present the data about the significant regions as follows:

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.

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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