SNP6 Copy number analysis (GISTIC2)

Esophageal Carcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

Maintainer Information

Citation Information

Maintained by Dan DiCara (Broad Institute)

Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C14B302S

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 2.0.21 (Firehose task version: 127).

Summary

There were 126 tumor samples used in this analysis: 24 significant arm-level results, 26 significant focal amplifications, and 49 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 - 26 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
11q13.3	1.1301e-79	1.1396e-79	chr11:69440355-70248899	11
8q24.21	4.1282e-23	4.1282e-23	chr8:128173711-128376800	0 [POU5F1B]
3q26.2	1.0438e-14	1.0438e-14	chr3:169464943-169746250	9
17q12	3.8697e-10	3.8697e-10	chr17:37737138-37930169	11
7q21.2	5.5783e-10	6.2951e-10	chr7:90968624-93866540	27
7p11.2	1.7534e-10	4.1659e-08	chr7:54815172-55550593	4
6p21.1	1.2944e-06	1.2944e-06	chr6:43582177-43989449	8
12p12.1	1.745e-05	9.5851e-05	chr12:24880663-25593511	6
18q11.2	0.00010682	0.00010682	chr18:20664008-21950411	12
19p13.2	0.00094834	0.00094834	chr19:7304493-7398264	0 [INSR]
19q12	0.00098323	0.00098323	chr19:30207925-30530934	2
1q21.3	0.0014471	0.0014471	chr1:151428606-152214419	23
8p11.21	5.2646e-05	0.002425	chr8:42155813-42504952	6
5p15.33	0.0026899	0.0026899	chr5:1287541-1348797	3
11p13	0.0042057	0.0046668	chr11:34463557-35306892	8
2q14.2	0.0095269	0.0095269	chr2:117933951-122704802	26
1p34.2	0.034012	0.034012	chr1:39565350-41984260	40
13q22.1	0.064093	0.064093	chr13:73630621-74211967	1
18p11.32	0.085294	0.085294	chr18:1-5430255	32
8p11.23	0.0011293	0.10245	chr8:35944476-38852435	26
10p11.21	0.10491	0.10491	chr10:35160206-35328433	1
12p13.33	0.040934	0.14039	chr12:1-1037287	12
9p13.3	0.14325	0.14325	chr9:31197602-37795391	106
7p22.3	0.025707	0.16015	chr7:1-22165420	135
6q23.3	0.1761	0.1761	chr6:135500891-135715565	3
15q26.3	0.20016	0.20016	chr15:89274202-102531392	98

Genes in Wide Peak

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

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

Genes
CCND1
hsa-mir-548k
CTTN
FGF3
FGF4
PPFIA1
FADD
FGF19
ANO1
ORAOV1
MIR548K

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
TERC
SEC62
MYNN
LRRC31
ARPM1
LRRC34
LRRIQ4
SAMD7
LOC100128164

Genes in Wide Peak

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

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

Genes
ERBB2
GRB7
NEUROD2
PNMT
TCAP
STARD3
IKZF3
PPP1R1B
MIEN1
PGAP3
MIR4728

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q21.2.

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

Genes
CDK6
AKAP9
hsa-mir-489
hsa-mir-1285-1
CALCR
KRIT1
CYP51A1
GNG11
GNGT1
PEX1
MTERF
TFPI2
BET1
ANKIB1
SAMD9
CCDC132
GATAD1
RBM48
MGC16142
SAMD9L
HEPACAM2
FAM133B
LRRD1
MIR489
MIR653
LOC728066
MIR4652

Genes in Wide Peak

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

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

Genes
EGFR
SEC61G
LANCL2
VOPP1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p21.1.

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

Genes
POLH
VEGFA
MAD2L1BP
GTPBP2
MRPS18A
C6orf223
RSPH9
LOC100132354

Genes in Wide Peak

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

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

Genes
KRAS
BCAT1
LRMP
CASC1
LYRM5
C12orf77

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18q11.2.

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

Genes
hsa-mir-320c-2
LAMA3
NPC1
RIOK3
CABYR
C18orf8
TMEM241
CABLES1
OSBPL1A
TTC39C
ANKRD29
MIR320C2

Genes in Wide Peak

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

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

Genes
CCNE1
URI1

Genes in Wide Peak

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

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

Genes
hsa-mir-554
RORC
S100A10
S100A11
TCHH
TUFT1
TDRKH
CELF3
POGZ
OAZ3
CGN
MRPL9
SNX27
THEM4
TCHHL1
RPTN
RIIAD1
THEM5
LINGO4
HRNR
MIR554
LOC100132111
C2CD4D

Genes in Wide Peak

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

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

Genes
IKBKB
POLB
SLC20A2
VDAC3
DKK4
C8orf40

Genes in Wide Peak

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

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

Genes
TERT
CLPTM1L
MIR4457

Genes in Wide Peak

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

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

Genes
CAT
CD44
ELF5
SLC1A2
PDHX
EHF
APIP
MIR1343

Genes in Wide Peak

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

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

Genes
DBI
EN1
GLI2
INHBB
PTPN4
RALB
SCTR
TSN
MARCO
DDX18
CLASP1
TFCP2L1
INSIG2
CCDC93
STEAP3
EPB41L5
TMEM185B
TMEM177
MKI67IP
LOC84931
C2orf76
TMEM37
C1QL2
PCDP1
LOC254128
RNU4ATAC

Genes in Wide Peak

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

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

Genes
MYCL1
hsa-mir-30c-1
BMP8B
COL9A2
CTPS
EDN2
NFYC
PPT1
RLF
PABPC4
KCNQ4
RIMS3
ZMPSTE24
PPIE
CAP1
SCMH1
MACF1
HEYL
HPCAL4
TRIT1
HIVEP3
OXCT2
SMAP2
DEM1
ZNF643
NT5C1A
MFSD2A
TMCO2
ZNF684
CITED4
SLFNL1
ZNF642
BMP8A
MIR30C1
MIR30E
KIAA0754
SNORA55
PPIEL
LOC100130557
LOC100507178

Genes in Wide Peak

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

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

Genes
KLF5

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18p11.32.

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

Genes
ADCYAP1
CETN1
TGIF1
TYMS
YES1
ZFP161
MYOM1
USP14
DLGAP1
LPIN2
THOC1
NDC80
MYL12A
EPB41L3
SMCHD1
CLUL1
ENOSF1
LINC00470
METTL4
COLEC12
EMILIN2
MYL12B
LINC00526
LOC201477
LOC284215
LOC339290
C18orf56
C18orf42
CBX3P2
FLJ35776
ROCK1P1
LOC727896

Genes in Wide Peak

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

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

Genes
FGFR1
WHSC1L1
ADRB3
EIF4EBP1
STAR
TACC1
ASH2L
BAG4
ERLIN2
PROSC
DDHD2
GPR124
LSM1
BRF2
PLEKHA2
ZNF703
RAB11FIP1
TM2D2
PPAPDC1B
GOT1L1
LETM2
KCNU1
HTRA4
RNF5P1
C8orf86
LOC728024

Genes in Wide Peak

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

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

Genes
CUL2

Genes in Wide Peak

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

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

Genes
KDM5A
NINJ2
RAD52
SLC6A12
SLC6A13
WNK1
CCDC77
B4GALNT3
IQSEC3
LOC574538
FAM138D
LOC100288778

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p13.3.

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

Genes
FANCG
PAX5
ACO1
ANXA2P2
NUDT2
AQP3
AQP7
BAG1
CA9
CCIN
CD72
CLTA
CNTFR
GALT
B4GALT1
DNAJA1
IL11RA
NDUFB6
NFX1
NPR2
PRSS3
RMRP
CCL19
CCL21
TESK1
TLN1
TPM2
VCP
RECK
GRHPR
RGP1
MELK
RUSC2
ZBTB5
GNE
TOPORS
SIGMAR1
CREB3
UNC13B
CCL27
PTENP1
DCTN3
FRMPD1
KIAA1045
DDX58
DNAJB5
DCAF12
SPAG8
FBXO10
DNAI1
SIT1
SPINK4
STOML2
EXOSC3
UBAP1
CHMP5
TMEM8B
APTX
UBE2R2
SMU1
UBAP2
OR2S2
KIAA1161
GBA2
POLR1E
NOL6
FAM214B
ZCCHC7
HINT2
C9orf24
PIGO
C9orf100
FP588
TAF1L
ARID3C
C9orf23
C9orf131
RNF38
GLIPR2
RG9MTD3
LOC158376
ATP8B5P
C9orf25
CCDC107
FAM205A
KIF24
ENHO
FAM205B
C9orf128
OR13J1
TMEM215
TOMM5
LOC415056
SUGT1P1
ANKRD18B
HRCT1
MSMP
FAM166B
SNORD121A
SNORD121B
LOC100129250
LOC100506710
MIR4667
MIR4540
MIR4475
MIR4476

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p22.3.

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

Genes
ETV1
PMS2
CARD11
hsa-mir-1183
hsa-mir-3146
hsa-mir-1302-6
hsa-mir-589
hsa-mir-339
ACTB
AHR
DGKB
GNA12
GPER
ICA1
ITGB8
LFNG
MEOX2
NUDT1
NDUFA4
PDGFA
PRKAR1B
RAC1
RPA3
FSCN1
SP4
TWIST1
ZNF12
AIMP2
MAFK
MAD1L1
EIF3B
DNAH11
CYTH3
PHF14
HDAC9
RAPGEF5
KIAA0415
ARL4A
AGR2
KDELR2
ADAP1
SNX13
IQCE
SUN1
SOSTDC1
WIPI2
INTS1
TSPAN13
EIF2AK1
BZW2
SNX8
FTSJ2
NXPH1
GET4
CCZ1
MIOS
RNF216
TMEM106B
ZNF853
CYP2W1
HEATR2
ZDHHC4
CHST12
CDCA7L
RADIL
PAPOLB
C1GALT1
FAM20C
ANKMY2
RBAK
C7orf26
MICALL2
FBXL18
TTYH3
USP42
PSMG3
C7orf50
TNRC18
C7orf70
SCIN
ZFAND2A
COX19
GLCCI1
KIAA1908
GPR146
AMZ1
AGR3
PER4
TMEM184A
VWDE
PRPS1L1
TWISTNB
SP8
BRAT1
SDK1
FOXK1
MMD2
DAGLB
CCZ1B
THSD7A
FERD3L
RPL23P8
SLC29A4
RSPH10B
TMEM196
TFAMP1
UNCX
COL28A1
ABCB5
MACC1
LOC389458
ELFN1
AGMO
GRID2IP
ZNF815
RNF216P1
PMS2CL
FLJ44511
LOC442497
MIR339
ZNF890P
OCM
MIR589
RSPH10B2
LOC729852
ISPD
LOC100131257
LOC100288524
MIR3146
LOC100506025
LRRC72
RBAK-LOC389458
MIR4648
MIR4655
MIR4656

Genes in Wide Peak

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

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

Genes
MYB
hsa-mir-548a-2
AHI1

Genes in Wide Peak

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

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

Genes
BLM
IDH2
CRTC3
hsa-mir-1302-10
hsa-mir-1469
hsa-mir-3175
hsa-mir-3174
hsa-mir-9-3
ACAN
ALDH1A3
ANPEP
CHD2
FES
IGF1R
MAN2A2
MEF2A
MFGE8
FURIN
PCSK6
PLIN1
POLG
RLBP1
SNRPA1
NR2F2
ST8SIA2
PEX11A
IQGAP1
PRC1
SV2B
AP3S2
SEMA4B
CIB1
ABHD2
CHSY1
SYNM
GABARAPL3
VPS33B
OR4F4
SLCO3A1
NGRN
RHCG
LINS
FANCI
MCTP2
SELS
MESP1
UNC45A
RGMA
WDR93
TTC23
LRRK1
TM2D3
C15orf42
RCCD1
ARRDC4
LOC91948
TARSL2
LRRC28
ASB7
LYSMD4
PGPEP1L
LOC145820
C15orf32
HAPLN3
MESP2
SPATA8
ADAMTS17
DNM1P46
CERS3
LOC254559
LOC283761
FAM169B
ZNF774
C15orf38
KIF7
ZNF710
HDDC3
WASH3P
FLJ42289
C15orf58
OR4F6
OR4F15
FAM174B
LOC400456
MIR9-3
TTLL13
ASB9P1
FAM138E
LOC100144604
GPCRLTM7
DDX11L1
DDX11L9
MIR1469
MIR3175
LOC100507217
LOC100507472
C15orf38-AP3S2
MIR4714

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 - 49 significant deletions found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband	Q value	Residual Q value	Wide Peak Boundaries	# Genes in Wide Peak
9p21.3	6.6983e-111	6.6983e-111	chr9:21865498-21997722	2
16q23.1	7.5664e-43	7.5664e-43	chr16:78129058-79627770	1
2q22.1	1.0892e-24	5.3639e-23	chr2:139655617-143637838	1
Xp21.1	3.102e-20	1.3809e-19	chrX:30870233-32665140	3
4q22.1	5.5492e-20	1.1095e-18	chr4:91148280-93240505	1
7q31.1	7.7396e-21	3.1448e-18	chr7:110725672-111366370	1
8p23.2	2.8897e-12	2.8897e-12	chr8:2079140-6262191	1
6p25.3	9.7557e-12	9.7557e-12	chr6:1608837-2252425	2
5q11.2	1.626e-11	1.4025e-10	chr5:58260298-59787985	3
3p14.2	1.3781e-13	7.2865e-09	chr3:59034763-61547330	1
18q21.2	1.3658e-09	3.367e-08	chr18:48472083-48705371	2
10p11.21	1.0173e-06	3.1458e-06	chr10:34059131-35328087	1
4p15.2	0.00014129	0.00014465	chr4:20727465-22330985	2
1p13.2	0.00012188	0.00016923	chr1:113498011-116379400	26
11q24.3	0.00017549	0.00017409	chr11:130014370-135006516	21
Xp11.3	3.1458e-06	0.00017409	chrX:44702452-45008304	2
3p14.3	1.477e-06	0.00047143	chr3:53923579-55500153	3
20p12.1	0.00055009	0.00058403	chr20:14302876-16252980	3
1q44	0.0009959	0.00093806	chr1:245864790-247052144	6
19p13.3	0.0010604	0.001066	chr19:1-2389783	100
18q12.2	5.5013e-05	0.0015512	chr18:35235531-39060470	4
10q23.31	0.0015512	0.0030651	chr10:89506488-92501260	31
13q14.2	0.00080579	0.0069209	chr13:48833767-49064807	2
6q26	0.0025642	0.0082059	chr6:161693099-163153207	1
2q33.3	0.00017409	0.0097682	chr2:204826225-206558638	1
Xq21.33	0.0096929	0.0097682	chrX:96134519-98718611	1
3q26.31	0.011833	0.011464	chr3:173999806-175760559	2
11p15.4	0.016814	0.016429	chr11:1-7045657	221
21q22.12	0.012671	0.016429	chr21:36154821-36413738	2
17q25.3	0.022497	0.022376	chr17:78935198-81195210	77
7q36.2	4.1061e-07	0.023846	chr7:140301332-159138663	183
3q11.1	0.00099948	0.027667	chr3:89525001-93777876	3
1p36.13	0.020895	0.029572	chr1:1-32119430	509
22q11.1	0.031511	0.031511	chr22:1-18562887	26
6q16.3	0.021506	0.037124	chr6:66030452-119138282	223
15q11.2	0.045059	0.046453	chr15:1-31198928	157
10p15.1	0.019834	0.064025	chr10:1-10831373	57
3p25.3	0.00032087	0.080797	chr3:11303687-11833472	2
21q11.2	0.066258	0.08784	chr21:1-26218513	44
5q15	0.014343	0.11843	chr5:65010846-127593809	262
17p11.2	0.12802	0.12938	chr17:11896630-25626166	126
13q12.11	0.0064309	0.15282	chr13:1-41025183	132
19q13.31	0.15862	0.15439	chr19:16431362-59128983	1127
13q21.2	0.055837	0.16388	chr13:52766125-115169878	182
12q21.2	0.19164	0.18649	chr12:71314430-133851895	454
4q31.3	0.022291	0.20612	chr4:152680887-153433684	3
4q21.23	0.003372	0.22281	chr4:85927963-87517209	3
10q22.3	0.072181	0.24066	chr10:39064001-135534747	727
14q31.1	0.23731	0.24066	chr14:53617998-107349540	512

Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53

Genes in Wide Peak

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

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

Genes
WWOX

Genes in Wide Peak

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

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

Genes
LRP1B

Genes in Wide Peak

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

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

Genes
hsa-mir-548f-5
DMD
FTHL17

Genes in Wide Peak

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

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

Genes
FAM190A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q31.1.

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

Genes
LRRN3

Genes in Wide Peak

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

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

Genes
CSMD1

Genes in Wide Peak

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

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

Genes
FOXC1
GMDS

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q11.2.

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

Genes
hsa-mir-582
PDE4D
PART1

Genes in Wide Peak

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

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

Genes
FHIT

Genes in Wide Peak

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

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

Genes
SMAD4
ELAC1

Genes in Wide Peak

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

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

Genes
PARD3

Genes in Wide Peak

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

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

Genes
KCNIP4
KCNIP4-IT1

Genes in Wide Peak

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

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

Genes
NRAS
TRIM33
AMPD1
CASQ2
NGF
SYCP1
TSHB
CSDE1
LRIG2
TSPAN2
BCAS2
AP4B1
PHTF1
PTPN22
RSBN1
OLFML3
DCLRE1B
SIKE1
VANGL1
SYT6
DENND2C
HIPK1
MAGI3
BCL2L15
LOC643441
LOC100287722

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q24.3.

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

Genes
OPCML
ST14
ADAMTS8
IGSF9B
NCAPD3
ACAD8
B3GAT1
ZBTB44
THYN1
NTM
JAM3
GLB1L2
VPS26B
GLB1L3
ADAMTS15
SPATA19
LOC283174
LOC283177
SNX19
LOC100128239
MIR4697

Genes in Wide Peak

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

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

Genes
KDM6A
DUSP21

Genes in Wide Peak

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

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

Genes
CACNA2D3
LRTM1
ESRG

Genes in Wide Peak

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

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

Genes
FLRT3
MACROD2
MACROD2-AS1

Genes in Wide Peak

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

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

Genes
SCCPDH
TFB2M
SMYD3
LOC149134
CNST
LOC255654

Genes in Wide Peak

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

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

Genes
STK11
TCF3
FSTL3
hsa-mir-4321
hsa-mir-1909
hsa-mir-3187
hsa-mir-1302-11
AMH
ATP5D
AZU1
HCN2
BSG
CDC34
CIRBP
CNN2
CSNK1G2
CFD
ARID3A
EFNA2
ELANE
GAMT
MKNK2
GPX4
GZMM
OAZ1
PALM
POLR2E
POLRMT
PRTN3
PTBP1
RPS15
MADCAM1
SF3A2
PPAP2C
AP3D1
MED16
APC2
ABCA7
UQCR11
SBNO2
HMHA1
SHC2
DAZAP1
FGF22
THEG
LSM7
MBD3
MIER2
PCSK4
C19orf24
PLEKHJ1
BTBD2
RNF126
SPPL2B
WDR18
REXO1
LPPR3
OR4F17
FAM108A1
KLF16
DOT1L
KISS1R
MUM1
MIDN
R3HDM4
C19orf6
TPGS1
REEP6
IZUMO4
SCAMP4
ADAT3
GRIN3B
JSRP1
MOB3A
C19orf21
PLK5
C2CD4C
CIRBP-AS1
C19orf25
ATP8B3
C19orf26
CSNK1G2-AS1
ODF3L2
ADAMTSL5
NDUFS7
C19orf35
WASH5P
ONECUT3
MEX3D
FLJ45445
PRSS57
FAM138F
LINGO3
FAM138A
LOC100288123
MIR1909
MIR1227
MIR3187
MIR4321
MIR4745

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q12.2.

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

Genes
hsa-mir-924
hsa-mir-4318
LOC647946
MIR4318

Genes in Wide Peak

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

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

Genes
PTEN
hsa-mir-107
ACTA2
FAS
IFIT2
IFIT1
IFIT3
LIPA
LIPF
CH25H
KIF20B
IFIT5
PANK1
RNLS
STAMBPL1
ATAD1
ANKRD22
LIPJ
CFL1P1
FLJ37201
LIPM
SLC16A12
MIR107
IFIT1B
LIPK
LIPN
LOC643529
KLLN
FAS-AS1
MIR4679-1
MIR4679-2

Genes in Wide Peak

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

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

Genes
RB1
LPAR6

Genes in Wide Peak

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

Table S48. 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 2q33.3.

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

Genes
PARD3B

Genes in Wide Peak

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

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

Genes
RPA4

Genes in Wide Peak

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

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

Genes
NAALADL2
MIR4789

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.4.

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

Genes
CARS
HRAS
NUP98
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
AP2A2
APBB1
RHOG
ART1
ASCL2
CCKBR
CD81
CD151
CDKN1C
TPP1
CNGA4
CTSD
DRD4
DUSP8
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INS
IRF7
KCNQ1
LSP1
MUC2
MUC6
NAP1L4
SLC22A18
SLC22A18AS
POLR2L
PSMD13
RNH1
MRPL23
RPLP2
RRM1
SCT
SMPD1
TRIM21
STIM1
TAF10
TALDO1
TH
TSPAN4
TNNI2
TNNT3
TRPC2
PHLDA2
ZNF195
ZNF214
ZNF215
RASSF7
IFITM1
OR6A2
DCHS1
BRSK2
TSPAN32
TSSC4
TRIM22
IFITM3
DEAF1
IFITM2
TRIM3
OR7E12P
KCNQ1OT1
PKP3
RRP8
SIRT3
OR52A1
ARFIP2
FXC1
PGAP2
C11orf21
TRPM5
UBQLN3
IGF2-AS1
BET1L
CEND1
TRIM34
CDHR5
TOLLIP
TRIM68
PIDD
KCNQ1DN
MMP26
CHRNA10
PNPLA2
PHRF1
SIGIRR
RIC8A
MRPL17
EPS8L2
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
MOB2
FAM160A2
TRIM5
SYT8
PRKCDBP
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
TRIM78P
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
LOC143666
OR10A5
OR2AG1
DNHD1
SCGB1C1
C11orf42
NLRP6
NS3BP
OR56B4
LOC255512
OR52B2
C11orf35
OR51F1
OR51B5
OR51V1
H19
EFCAB4A
TMEM80
OR10A4
C11orf36
ANO9
LOC338651
B4GALNT4
OR52L1
OR2AG2
OR52B6
OR10A2
PDDC1
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR56B1
GVINP1
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TRIM6-TRIM34
MIR483
SNORA52
LOC650368
LOC653486
SNORA54
INS-IGF2
MUC5B
MIR675
FAM99B
LOC100133161
MRPL23-AS1
MIR4298
MIR210HG
MIR4686
MIR4687

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.12.

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

Genes
RUNX1
RUNX1-IT1

Genes in Wide Peak

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

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

Genes
ASPSCR1
hsa-mir-3186
hsa-mir-1250
ACTG1
ARHGDIA
CD7
CSNK1D
SLC25A10
FASN
GCGR
UTS2R
GPS1
FOXK2
MAFG
P4HB
PDE6G
PYCR1
PCYT2
RAC3
RFNG
MRPL12
SECTM1
TBCD
SLC16A3
HGS
AATK
ALYREF
BAIAP2
RAB40B
AZI1
FSCN2
NARF
DCXR
ANAPC11
SIRT7
NPLOC4
WDR45L
BAHCC1
DUS1L
FN3K
C17orf62
CHMP6
FN3KRP
C17orf101
ZNF750
C17orf70
TSPAN10
MAFG-AS1
PPP1R27
SLC38A10
C17orf56
B3GNTL1
NOTUM
STRA13
LRRC45
MYADML2
NPB
CCDC57
HEXDC
C17orf89
LINC00482
TMEM105
METRNL
C17orf90
CCDC137
ARL16
FAM195B
AATK-AS1
FLJ43681
TEX19
FLJ90757
MIR338
MIR657
MIR1250
MIR3065
MIR3186
MIR4740

Genes in Wide Peak

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

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

Genes
BRAF
EZH2
MLL3
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
ABP1
CASP2
CDK5
CLCN1
DPP6
EN2
EPHA1
EPHB6
GBX1
MNX1
HTR5A
INSIG1
KCNH2
KEL
NDUFB2
NOS3
PIP
PRSS1
PRSS2
TAS2R38
PTPRN2
RARRES2
RHEB
SHH
SLC4A2
SMARCD3
SSBP1
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
MGAM
ACCN3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
FASTK
ABCB8
PAXIP1
SSPO
CLEC5A
CNTNAP2
GIMAP2
OR2F1
TPK1
ZNF777
TMEM176B
REPIN1
TAS2R3
TAS2R4
PRKAG2
MRPS33
NUB1
TAS2R5
CHPF2
NCAPG2
WDR60
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
TRPV5
ACTR3B
KIAA1147
ESYT2
ZNF398
GALNT11
LMBR1
LINC00244
NOM1
LRRC61
ZNF767
TMUB1
KRBA1
OR6W1P
ADCK2
LOC93432
C7orf29
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
ASB10
PRSS58
RNF32
TRY6
LOC154761
LOC154822
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
GALNTL5
GIMAP7
ZNF467
GIMAP1
LOC202781
C7orf33
FABP5P3
TAS2R39
TAS2R40
TAS2R41
CNPY1
LOC285889
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
TAS2R60
CTAGE6P
OR6V1
OR2A12
OR2A1
WDR86
GSTK1
OR2A25
OR2A5
OR2A7
OR2A20P
LOC401431
OR2A42
MIR153-2
CTAGE15P
OR2A9P
OR2A2
ARHGEF35
GIMAP6
WEE2
ZNF862
LOC645249
ACTR3C
MIR595
LOC728377
LOC728743
LOC730441
MIR671
LOC100124692
LOC100128264
CTAGE4
LOC100128822
LOC100131176
LOC100132707
LOC100134713
MOXD2P
ZNF783
MIR548F3
MIR548I4
MIR548F4
MIR548T
MTRNR2L6
MIR3907
LOC100505483
LOC100506585
LOC100507421
GIMAP1-GIMAP5

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q11.1.

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

Genes
PROS1
ARL13B
STX19

Genes in Wide Peak

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

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

Genes
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
ALPL
RERE
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
MEGF6
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FABP3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
HCRTR1
ZBTB48
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MATN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SRSF4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
SNHG3
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
AKR7A2
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
SNRNP40
C1orf38
H6PD
ISG15
PLCH2
SDC3
CROCC
PUM1
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
GMEB1
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
TMEM50A
STX12
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
RNU11
HSPB7
ARHGEF16
AHDC1
SMPDL3B
PRO0611
LINC00339
SSU72
UBIAD1
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF593
MECR
SDF4
MRTO4
YTHDF2
ZCCHC17
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
XKR8
ARHGEF10L
VPS13D
ATAD3A
TMEM57
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
TINAGL1
PLA2G2F
CEP85
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
PHACTR4
C1orf135
EFHD2
MMEL1
RSG1
OR4F5
NKAIN1
MUL1
NOL9
LIN28A
AGMAT
LINC00115
MORN1
FAM110D
DHDDS
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
C1orf170
CROCCP2
SYTL1
IGSF21
SNHG12
KIAA1751
KIAA2013
THAP3
C1orf201
UBXN11
C1orf158
FBXO44
ATPIF1
CROCCP3
FHAD1
LOC115110
RAB42
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
LOC149086
PDIK1L
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
C1orf126
ATAD3C
AKR7L
LOC254099
TTLL10
TMCO4
ZNF683
NPHP4
LOC284551
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
TMEM240
TMEM52
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
SERINC2
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
CATSPER4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
RNF223
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
ANKRD65
PRAMEF7
PEF1
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA1
SNORA44
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD85
SNORD99
SNORD103A
SNORD103B
MIR551A
CDK11A
SLC35E2B
LOC728716
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100129196
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
NPPA-AS1
MIR3115
MIR4253
MIR4251
MIR4252
MIR3917
MIR3675
ENO1-AS1
LOC100506730
LOC100506801
LOC100506963
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4420
MIR4684
MIR4689
MIR4632
MIR4417
MIR378F
RCAN3AS

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q11.1.

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

Genes
hsa-mir-648
hsa-mir-3198
ATP6V1E1
BID
IL17RA
ANKRD62P1-PARP4P3
POTEH
BCL2L13
HSFY1P1
CECR6
CECR5
CECR3
CECR2
CECR1
MICAL3
OR11H1
SLC25A18
GAB4
CCT8L2
XKR3
TPTEP1
MIR648
CECR7
CECR5-AS1
FLJ41941
MIR3198-1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q16.3.

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

Genes
PRDM1
ROS1
GOPC
hsa-mir-587
hsa-mir-2113
hsa-mir-4282
hsa-mir-30a
hsa-mir-30c-2
AIM1
AMD1
BAI3
BCKDHB
CCNC
CGA
CNR1
COL9A1
COL10A1
COL12A1
COL19A1
COX7A2
EEF1A1
EPHA7
FOXO3
FRK
FYN
GABRR1
GABRR2
GPR6
GRIK2
HDAC2
HTR1B
HTR1E
IMPG1
KPNA5
LAMA4
MARCKS
ME1
MYO6
NT5E
PGM3
PLN
POU3F2
PREP
REV3L
RNY4
SIM1
SMPD2
ELOVL4
MAP3K7
NR2E1
TPBG
TSPYL1
TTK
DDO
SNX3
RNGTT
CD164
WISP3
WASF1
TBX18
HMGN3
FHL5
ATG5
ZBTB24
SNAP91
FIG4
CASP8AP2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
MDN1
TSPYL4
UFL1
ORC3
BRD7P3
MTO1
PNISR
IBTK
SENP6
FBXL4
SLC17A5
SNORD50A
FILIP1
SESN1
OSTM1
NDUFAF4
DSE
CYB5R4
TUBE1
C6orf203
CDC40
RWDD1
UBE2J1
COQ3
PHIP
SOBP
AKIRIN2
QRSL1
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
LMBRD1
KCNQ5
RARS2
PDSS2
C6orf162
LYRM2
SNX14
HACE1
FAM135A
BEND3
RRAGD
PRDM13
BACH2
SMAP1
C6orf164
POPDC3
MICAL1
OGFRL1
MANEA
LINC00472
KHDC1
GPR63
SPACA1
SH3BGRL2
ARMC2
RPF2
MCHR2
FAXC
GJA10
RTN4IP1
USP45
SLC22A16
C6orf7
UBE2CBP
KIAA1919
GTF3C6
MRAP2
RWDD2A
KLHL32
MB21D1
NUS1
SLC16A10
RIPPLY2
IRAK1BP1
B3GAT2
C6orf57
CD109
PM20D2
SRSF12
C6orf221
C6orf165
BVES-AS1
PRSS35
LCA5
C6orf163
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
HS3ST5
GPRC6A
RFX6
SLC35F1
VGLL2
LACE1
MMS22L
FAM26E
SCML4
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
DPPA5
RSPH4A
EYS
GJB7
SNHG5
C6orf147
LINC00222
CEP85L
LIN28B
MIR30A
MIR30C2
OOEP
FAM26F
MCART3P
GSTM2P1
RFPL4B
C6orf225
TSG1
TRAF3IP2-AS1
SNORD50B
LOC728012
TPI1P3
C6orf186
BET3L
KHDC1L
LOC100130890
LOC100287632
LOC100288198
MIR2113
MIR548H3
LOC100422737
MIR4282
LOC100506804
MIR4464
MIR4643

Genes in Wide Peak

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

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

Genes
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
APBA2
NBEAP1
GABRA5
GABRB3
GABRG3
IPW
NDN
OCA2
SNRPN
TJP1
UBE3A
MKRN3
PAR5
HERC2
SNURF
CYFIP1
FAM189A1
C15orf2
DKFZP434L187
MAGEL2
NDNL2
ATP10A
NIPA2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
SNORD107
TUBGCP5
NIPA1
PAR1
LOC283683
OR4N4
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
SNORD64
PAR4
PAR-SN
LOC348120
GOLGA8E
OR4M2
OR4N3P
HERC2P2
NF1P2
HERC2P9
WHAMMP2
LOC503519
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
SNORD116-19
GOLGA6L6
LOC727924
GOLGA8C
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
LOC100128714
HERC2P7
GOLGA8F
GOLGA8DP
ULK4P2
LOC100288637
LOC100289656
MIR4509-1
MIR4509-2
MIR4508
MIR4509-3
MIR4715

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p15.1.

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

Genes
GATA3
hsa-mir-3155
ADARB2
ATP5C1
CALML3
AKR1C4
KLF6
AKR1C1
AKR1C2
GDI2
IDI1
IL2RA
IL15RA
ITIH2
PFKFB3
PFKP
PRKCQ
AKR1C3
NET1
PITRM1
ZMYND11
WDR37
KIN
DIP2C
LARP4B
GTPBP4
CALML5
ANKRD16
FAM208B
IDI2-AS1
SFMBT2
ASB13
TUBAL3
ITIH5
AKR1E2
TAF3
FBXO18
RBM17
IDI2
UCN3
LOC282980
LOC338588
AKR1CL1
TUBB8
tAKR
LINC00200
LOC399708
LOC399715
FLJ45983
C10orf108
LOC439949
ADARB2-AS1
LOC100216001
MIR3155A
LOC100507034
LOC100507127
MIR3155B

Genes in Wide Peak

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

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

Genes
VGLL4
ATG7

Genes in Wide Peak

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

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

Genes
hsa-mir-548x
hsa-mir-125b-2
hsa-let-7c
hsa-mir-3118-5
hsa-mir-3156-3
BAGE
CXADR
NCAM2
TMPRSS15
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
CHODL-AS1
C21orf15
LINC00308
C21orf91
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
CHODL
ANKRD30BP2
LIPI
ABCC13
C21orf91-OT1
D21S2088E
POTED
LINC00317
LINC00320
LOC388813
LINC00478
ANKRD20A11P
MIRLET7C
MIR125B2
MIR99A
TEKT4P2
MIR3156-3
MIR3687
MIR3648
C21orf37

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q15.

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

Genes
APC
PIK3R1
hsa-mir-1244-2
hsa-mir-548f-3
hsa-mir-548p
hsa-mir-583
hsa-mir-2277
hsa-mir-9-2
hsa-mir-4280
ARSB
ALDH7A1
BHMT
BTF3
CAMK4
CAST
CCNB1
CCNH
CDK7
CDO1
CETN3
CHD1
CKMT2
AP3S1
COX7C
CRHBP
HAPLN1
CSNK1G3
VCAN
DMXL1
DHFR
EFNA5
F2R
F2RL1
F2RL2
FER
FOXD1
GLRX
GTF2H2
HEXB
HMGCR
HSD17B4
KCNN2
TNPO1
LMNB1
LNPEP
LOX
CD180
MAN2A1
MAP1B
MCC
MEF2C
MSH3
NAIP
PAM
PCSK1
PGGT1B
PMCHL2
PPIC
RAD17
RASA1
RASGRF2
RPS23
SLC12A2
SMN1
SMN2
SNX2
SRP19
TAF9
TBCA
NR2F1
THBS4
XRCC4
ST8SIA4
REEP5
SERF1A
ENC1
AP3B1
PDE8B
ATG12
NREP
RAB9BP1
HOMER1
SCAMP1
CARTPT
SNCAIP
TTC37
ZFYVE16
PJA2
EDIL3
COL4A3BP
LHFPL2
NSA2
POLR3G
IQGAP2
SMA4
SMA5
RHOBTB3
ELL2
SV2C
MRPS27
PPIP5K2
OTP
SSBP2
BHMT2
TNFAIP8
FAM169A
RNU5E-1
RNU5D-1
SNX24
DMGDH
TMED7
GCNT4
PRR16
COMMD10
POLK
ERAP1
PHAX
FLJ11235
GIN1
AGGF1
WDR41
TRIM36
RIOK2
BDP1
ERBB2IP
FEM1C
NLN
ZNF608
SEMA6A
ARRDC3
ANKRA2
MCCC2
EPB41L4A
ERAP2
RGNEF
FBXL17
YTHDC2
SLC30A5
CENPH
GRAMD3
MCTP1
PTCD2
NUDT12
ATG10
SPATA9
TSSK1B
FAM172A
GPR98
UTP15
ZCCHC9
ANKRD32
ZBED3
GFM2
MEGF10
SPZ1
TSLP
C5orf30
SLC25A46
MRPS36
ATP6AP1L
PRDM6
FTMT
EPB41L4A-AS1
MARCH3
FCHO2
LYSMD3
SLCO6A1
PRRC1
JMY
ZNF474
POU5F2
TMEM171
TMEM174
POC5
STARD4
WDR36
ACOT12
SREK1
CEP120
TMEM167A
MBLAC2
TMEM161B
SRFBP1
MARVELD2
ARSK
FAM81B
CCDC112
PAPD4
DCP2
LIX1
ZNF366
FAM151B
S100Z
CCDC125
C5orf27
CMYA5
AQPEP
ANKRD31
SERINC5
KIAA0825
GPR150
DTWD2
NBPF22P
RGMB
RFESD
FAM170A
ANKRD34B
FAM174A
MTX3
SLCO4C1
TICAM2
MAST4
C5orf48
C5orf63
MIR9-2
CRSP8P
FLJ42709
FLJ35946
CTXN3
TMEM232
LOC644100
FLJ33630
LOC644936
LINC00461
LOC647859
GUSBP3
GTF2H2B
SNORA13
SCARNA18
SNORA47
MIR583
GTF2H2C
LOC728342
SERF1B
LOC728723
GTF2H2D
GUSBP9
LOC100129716
LOC100131067
LOC100133050
LOC100170939
LOC100272216
LOC100289230
LOC100289673
MIR1244-1
TMED7-TICAM2
NCRUPAR
LOC100303749
MIR2277
MIR1244-3
MIR1244-2
MIR4280
MTRNR2L2
MIR3607
MIR3660
LOC100505678
LOC100505841
LOC100505894
OCLN
MIR4804
MIR3977
MIR4803

Genes in Wide Peak

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

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

Genes
MAP2K4
hsa-mir-1180
hsa-mir-33b
hsa-mir-1288
hsa-mir-548h-3
hsa-mir-744
ADORA2B
ALDH3A1
ALDH3A2
COX10
DRG2
FOXO3B
FLII
KCNJ12
LLGL1
MEIS3P1
MFAP4
PMP22
MAPK7
MAP2K3
PRPSAP2
SHMT1
SREBF1
TOP3A
UBB
RNF112
COPS3
TMEM11
PIGL
NCOR1
ULK2
CCDC144A
ARHGAP44
HS3ST3B1
HS3ST3A1
PEMT
FBXW10
TRIM16
RAI1
GRAP
AKAP10
EPN2
MPRIP
USP22
TNFRSF13B
DHRS7B
SNORD49A
B9D1
FAM18B1
MYO15A
TRPV2
RASD1
ALKBH5
TTC19
MED9
SLC47A1
NT5M
ZNF286A
ZNF287
ZNF624
ELAC2
TEKT3
C17orf39
FAM106A
LRRC48
MGC12916
ATPAF2
SPECC1
MYOCD
CDRT7
CDRT15P1
C17orf76-AS1
ZSWIM7
SMCR7
SLC5A10
SMCR5
SMCR8
SMCR9
TOM1L2
SLC47A2
CDRT15
TRIM16L
USP32P1
FAM18B2
CENPV
FLCN
PLD6
USP32P2
TBC1D28
CDRT15L2
C17orf103
FLJ34690
CDRT4
CCDC144B
FAM27L
FLJ36000
LGALS9B
CCDC144NL
LOC339240
C17orf51
CCDC144C
TBC1D26
CDRT1
FAM211A
KRT16P2
GRAPL
CDRT15P2
FAM83G
KRT16P3
EVPLL
LGALS9C
SNORA59B
SNORA59A
SNORD49B
SNORD65
MIR33B
ZNF286B
MIR744
FAM106CP
KCNJ18
MIR1288
MIR1180
MTRNR2L1
FAM18B2-CDRT4
MIR4731
MIR4522

Genes in Wide Peak

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

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

Genes
BRCA2
CDX2
FLT3
LHFP
hsa-mir-4305
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
CDK8
FGF9
FLT1
GJA3
GJB2
GPR12
GTF3A
HMGB1
PDX1
MAB21L1
SMAD9
MIPEP
PABPC3
UBL3
RFC3
RFXAP
RNF6
RPL21
SGCG
SLC7A1
TRPC4
TUBA3C
ZMYM2
IFT88
CCNA1
MTMR6
DCLK1
ZMYM5
KL
NUPL1
FRY
USPL1
SAP18
N4BP2L2
POSTN
GJB6
HSPH1
WASF3
EXOSC8
PDS5B
SPG20
MTUS2
SACS
LATS2
SNORD102
NBEA
ALG5
POLR1D
CRYL1
POMP
UFM1
ATP8A2
IL17D
MPHOSPH8
SOHLH2
PSPC1
TNFRSF19
FAM48A
CENPJ
RNF17
COG6
XPO4
MRP63
PROSER1
KATNAL1
C13orf33
STARD13
N4BP2L1
TPTE2
CG030
CSNK1A1L
RXFP2
TEX26
B3GALTL
STOML3
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
ZDHHC20
PAN3
PHF2P1
SLC46A3
ANKRD20A9P
C1QTNF9
FREM2
LINC00442
TPTE2P6
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERTM1
LINC00547
LINC00548
ATP5EP2
LOC440131
C1QTNF9B-AS1
SNORA27
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
CCDC169
ANKRD26P3
RPL21P28
LINC00426
LINC00421
PAN3-AS1
MIR548F5
MIR2276
MIR4305
LINC00327
TEX26-AS1
SPG20OS
CCDC169-SOHLH2
MIR4499

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.31.

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

Genes
AKT2
BCL3
CD79A
CEBPA
ERCC2
JAK3
KLK2
PPP2R1A
ELL
CIC
CBLC
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-935
hsa-mir-373
hsa-mir-1283-2
hsa-mir-643
hsa-mir-125a
hsa-mir-150
hsa-mir-4324
hsa-mir-220c
hsa-mir-3191
hsa-mir-320e
hsa-mir-769
hsa-mir-642
hsa-mir-4323
hsa-mir-641
hsa-mir-1270-2
hsa-mir-1270-1
hsa-mir-640
hsa-mir-3189
hsa-mir-3188
A1BG
ACTN4
AP2A1
APLP1
APOC1
APOC1P1
APOC2
APOC4
APOE
KLK3
ATP1A3
ATP4A
AXL
BAX
BCAT2
BCKDHA
CEACAM1
BLVRB
BST2
C5AR1
CA11
CALM3
CAPNS1
CCNE1
CD22
CD33
SIGLEC6
CD37
CEACAM5
CEBPG
CGB
CEACAM3
CEACAM7
CEACAM8
CEACAM4
TBCB
CKM
AP2S1
CLC
CLPTM1
COMP
COX6B1
COX7A1
CRX
NCAN
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2B7P1
CYP2F1
DBP
DMPK
DMWD
ECH1
MEGF8
EMP3
NR2F6
ERCC1
ERF
FBL
ETFB
ETV2
FCAR
FCGRT
FKBP1AP1
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GDF1
GIPR
GPI
GPR4
GPR32
FFAR1
FFAR3
FFAR2
GRIK5
GRIN2D
ARHGAP35
GSK3A
GYS1
HAS1
FOXA3
HNRNPL
HPN
HRC
PRMT1
IL11
IL12RB1
INSL3
IRF3
JUND
KCNA7
KCNC3
KCNJ14
KCNN1
KCNN4
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LGALS4
LGALS7
LHB
LIG1
LIM2
LIPE
LRP3
BCAM
MAG
MEF2BNB-MEF2B
MAP3K10
MYBPC2
MYO9B
CEACAM6
NDUFA3
NFKBIB
NKG7
CNOT3
NOVA2
NPAS1
NPHS1
NTF4
NUCB1
PAFAH1B3
PDE4C
PEG3
PEPD
PIK3R2
PLAUR
FXYD1
FXYD3
POLD1
POLR2I
POU2F2
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PSMC4
PSMD8
PTGIR
PTPRH
PVR
PVRL2
RAB3A
RELB
UPF1
RPL18
RPL18A
RPL28
MRPS12
RPS5
RPS9
RPS11
RPS16
RPS19
RRAS
RTN2
RYR1
CLEC11A
SCN1B
SEPW1
SLC1A5
SLC5A5
SLC8A2
SNRNP70
SNRPA
SNRPD2
SPIB
AURKC
SULT2B1
SULT2A1
SUPT5H
SYT5
TGFB1
TNNI3
TNNT1
TULP2
TYROBP
UBA52
NR1H2
UQCRFS1
USF2
VASP
XRCC1
ZFP36
ZNF8
ZNF14
ZNF708
ZNF17
ZNF28
MZF1
ZNF43
ZNF45
ZNF221
ZNF85
ZNF90
ZNF91
ZNF99
ZNF222
ZNF132
ZNF134
ZNF135
ZNF137P
ZNF146
ZNF154
ZNF155
ZNF175
ZNF180
ZNF208
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF230
SYMPK
MIA
DPF1
LTBP4
TEAD2
PPFIA3
PLA2G4C
RFXANK
URI1
NAPA
SIGLEC5
FCGBP
PGLYRP1
F2RL3
UBE2M
ARHGEF1
PDCD5
DYRK1B
LPAR2
CRLF1
NUMBL
CYTH2
ZNF235
ZNF264
KCNK6
NCR1
MED26
HOMER3
NAPSA
GDF15
ZNF254
GMFG
KLK4
ZNF432
DHX34
KIAA0355
ZNF536
MLL4
UBA2
SAE1
SUGP2
TRIM28
ZNF256
LILRB2
PAK4
B3GNT3
KLF2
TMEM147
IFI30
TOMM40
ZNF211
CHERP
RABAC1
TRAPPC2P1
SPINT2
DLL3
CERS1
POP4
ZNF234
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
HCST
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
UPK1A
HNRNPUL1
CLASRP
KPTN
SLC7A9
MAP4K1
KLK8
PNKP
COPE
U2AF2
ATF5
ZFP30
ZNF507
PPP6R1
CARD8
SIRT2
CYP2G1P
UNC13A
MAST3
SIPA1L3
FCHO1
ZC3H4
SIN3B
HAUS5
CRTC1
MAU2
FBXO46
ETHE1
RPL13A
SYNGR4
LILRA4
PRG1
ZIM2
NUP62
HSPBP1
PPP1R15A
PLD3
FKBP8
EML2
TMEM59L
PGLS
ZNF324
LSM4
KLK5
ZNF345
PRKD2
ZNF473
CLIP3
LSM14A
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
GAPDHS
SNORA68
SNORD35A
SNORD34
SNORD33
SNORD32A
ZNF285
ZBTB32
SIGLEC7
LYPD3
ARRDC2
BBC3
DKKL1
CPAMD8
SIGLEC9
SIGLEC8
GPR77
CHMP2A
DHDH
ZNF544
EIF3K
UBE2S
SLC6A16
BABAM1
LGALS13
CYP2S1
STRN4
CCDC106
EPN1
SERTAD3
SERTAD1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
NDUFA13
ZNF580
HSD17B14
GP6
VRK3
ZNF571
GMIP
ISYNA1
ZNF581
LSR
TM6SF2
PTOV1
FXYD7
FXYD5
RAB4B
DDX49
PAF1
PPP1R12C
TRPM4
ZNF586
QPCTL
GATAD2A
FAM83E
PGPEP1
EPS8L1
RASIP1
TMEM161A
SARS2
TMEM160
PIH1D1
C19orf60
GPATCH1
SAMD4B
ATP5SL
C19orf73
MAP1S
PNMAL1
TMEM143
KLHL26
ZNF444
KLK15
MED29
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
USE1
PSENEN
ZNF302
LIN37
SMG9
ZNF253
IRGC
SLC7A10
CABP5
SPHK2
LGALS14
EXOSC5
MEIS3
CEACAM19
SLC17A7
NAT14
CD177
ATP13A1
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
ZNF492
TSHZ3
LRFN1
GRAMD1A
USP29
PLEKHA4
ZFP14
ZNF529
PRX
ANO8
SPTBN4
MARK4
SUGP1
HAMP
CATSPERG
ZNF71
SCAF1
PRODH2
EPS15L1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
DMRTC2
C19orf33
ELSPBP1
LIN7B
HIF3A
CHST8
ZNF574
PLEKHG2
MRPL34
ZNF649
ZSCAN18
MGC2752
DDA1
KXD1
TMEM38A
TSEN34
KCTD15
C19orf42
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
PLEKHF1
LENG1
LILRP2
LILRA6
RBM42
ZNF576
LRFN3
ABHD8
OCEL1
ZNF329
GLT25D1
IGFLR1
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
ADCK4
CNTD2
SLC35E1
ZNF702P
LOC80054
ZNF606
ZNF614
FUZ
OPA3
ZNF430
ITPKC
PBX4
KIAA1683
B9D2
RSPH6A
ZNF611
MED25
ZNF93
PLVAP
BCL2L12
C19orf12
TEX101
GRWD1
USHBP1
WDR87
TSSK6
CCDC8
KIRREL2
ANKRD27
C19orf44
ZNF541
SYT3
PDCD2L
AKT1S1
ZNF528
BRSK1
ZNF527
CNFN
SNORD35B
ZNF347
GTPBP3
ZNF577
MPV17L2
ZNF607
SUV420H2
C19orf48
NFKBID
ZBTB45
CEP89
ZNF382
ZNF587
FIZ1
ZNF566
ALKBH6
RHPN2
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF30
ZNF551
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
ZNF835
YIF1B
ZNF486
ZNF682
C19orf40
TDRD12
ZNF765
NLRP12
MYADM
ZNF845
ZNF461
ZNF585B
TIMM50
SHKBP1
DMKN
CCDC114
HAUS8
FAM125A
DKFZp434J0226
ARMC6
ACPT
CGB5
DKFZp566F0947
CGB7
LRRC4B
ZNF101
LENG9
CGB8
GNG8
PPP1R14A
EGLN2
BIRC8
FAM71E1
RDH13
PTH2
ZNF257
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
CCDC124
FBXO17
KIR3DL3
ARHGAP33
RASGRP4
NXNL1
ZNF526
ZNF837
CLDND2
ZNF816
ZNF543
CEACAM20
COX6B2
CALR3
OSCAR
ZNF813
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZNF573
WDR88
EID2B
IRGQ
ZNF428
LRRC25
WTIP
ZNF792
NR2C2AP
HSPB6
RINL
FBXO27
C19orf47
ANKLE1
ZFP28
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
PPM1N
KLC3
IGSF23
LYPD4
TMEM190
HIPK4
TMC4
LOC147804
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
ZNF420
ZNF565
NLRP4
ZNF542
ZNF582
ZNF583
FAM98C
CAPN12
DPY19L3
LGALS16
TTC9B
ZNF599
FAM187B
CILP2
C19orf55
LOC148145
CDC42EP5
LOC148189
ZNF98
ZNF738
ZNF714
ZNF681
ZNF569
ZNF570
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF296
DEDD2
ZNF579
ZNF114
ZNF567
ZNF383
ZNF781
EID2
ZNF780B
LGI4
C19orf46
ZNF676
ZNF100
ZNF540
SSBP4
ZNF525
ZNF431
SPACA4
ZNF675
ZNF585A
NLRP7
GGN
CADM4
THAP8
U2AF1L4
ZNF626
FAM129C
C19orf76
ZNF584
ZSCAN4
NLRP11
TMEM86B
PRR24
ZNF549
NAPSB
IL4I1
IL28A
IL28B
IL29
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
ZNF780A
C19orf54
PRR19
TMEM145
CXCL17
LOC284344
ZNF575
LYPD5
ZNF283
PPP1R37
NKPD1
TPRX1
MAMSTR
IZUMO1
C19orf63
MGC45922
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
LOC284395
SCGB2B2
WDR62
ZFP82
LOC284408
LOC284412
VSTM1
TMEM150B
FAM71E2
NWD1
SLC25A42
LOC284440
ZNF493
HKR1
VN1R2
VN1R4
NLRP9
ZNF181
ZNF260
ZNF546
MYPOP
NANOS2
VSTM2B
ZNF850
NCCRP1
SYCN
LEUTX
ZNF404
ZNF284
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
SELV
ZNF530
C19orf51
ZNF429
ZNF233
LILRA5
YJEFN3
SBSN
ZNF829
ZNF568
B3GNT8
IGFL1
ZNF773
SLC27A1
LOC386758
RPSAP58
RGS9BP
KRTDAP
ZNF790
CEACAM22P
CEACAM16
BLOC1S3
LOC388553
IGFL3
ZNF808
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
NUDT19
ZNF793
PAPL
LOC390940
ZNF805
SPRED3
ZNF321P
LOC400680
LOC400684
LOC400685
LGALS17A
SIGLEC16
FLJ26850
ZNF880
ZNF772
IGLON5
HAPLN4
MIRLET7E
MIR125A
MIR150
MIR99B
ZNF506
LOC440518
ZNF724P
PSG8
TARM1
MIR330
MIR371A
MIR372
MIR373
IGFL4
A1BG-AS1
DPRX
DUXA
ASPDH
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
KLKP1
LOC641367
TMEM91
LOC643669
SCGB1B2P
SDHAF1
LOC644189
LOC644554
LOC646508
SBK2
LOC646862
PSG10P
LGALS7B
PHLDB3
SEC1
ZNF826P
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR641
MIR642A
MIR643
RPL13AP5
LOC728752
CCDC61
CEACAM18
SHISA7
LOC729966
FLJ30403
MEF2BNB
ZNF814
ZNF726
MIR769
SIGLEC14
MIMT1
LOC100101266
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
LOC100128252
LOC100128398
LOC100128675
LOC100128682
LOC100129083
ZNF737
LOC100129935
SCGB2B3P
TMEM221
SGK110
BSPH1
LOC100131691
LOC100134317
PEG3-AS1
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-B2
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-B1
SNAR-C1
SNAR-C3
SNAR-D
SNAR-G2
SRRM5
C19orf69
SNAR-A14
ERVV-2
MEF2B
LOC100287177
ZNF729
LOC100289650
ZNF587B
MIR1270-1
MIR1283-2
MIR1323
MIR1283-1
LOC100379224
MIR3191
MIR3188
MIR3190
MIR320E
MIR3189
MIR4324
MIR4323
MIR1270-2
MIR642B
LOC100505495
LOC100505622
LOC100505681
LOC100505715
LOC100505812
LOC100505835
LOC100506012
LOC100506033
LOC100506068
LOC100506469
LOC100506930
LOC100507003
ZNF865
LOC100507433
THEG5
ZNF816-ZNF321P
MIA-RAB4B
RAB4B-EGLN2
APOC4-APOC2
MIR4530
MIR4754
MIR4752
MIR371B
MIR4749
MIR4750
MIR4531
MIR4751
LOC100631378
LOC100652909

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q21.2.

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

Genes
ERCC5
hsa-mir-1267
hsa-mir-4306
hsa-mir-623
hsa-mir-3170
hsa-mir-92a-1
hsa-mir-622
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
ATP4B
KLF5
BTF3P11
CLN5
COL4A1
COL4A2
DACH1
DCT
GPR183
EDNRB
EFNB2
F7
F10
FGF14
GPC5
GAS6
GPR18
ING1
IPO5
LAMP1
LIG4
LMO7
PCCA
PCDH8
PCDH9
POU4F1
DNAJC3
RAP2A
GRK1
ATXN8OS
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
UCHL3
ZIC2
STK24
CUL4A
IRS2
SCEL
PROZ
ARHGEF7
CDC16
CLDN10
ITGBL1
TM9SF2
TBC1D4
GPC6
MBNL2
FARP1
SPRY2
ABCC4
TUBGCP3
PIBF1
OLFM4
TNFSF13B
SUGT1
LECT1
SOX21
KLF12
RASA3
DZIP1
DIS3
MYO16
MYCBP2
ATP11A
MCF2L
DOCK9
TGDS
SLITRK5
FBXL3
CKAP2
OXGR1
PCDH17
VPS36
NDFIP2
BIVM
TMCO3
ARGLU1
DCUN1D2
ANKRD10
RAB20
CARKD
UGGT2
PCID2
THSD1
KLHL1
RBM26
PCDH20
UPF3A
KDELC1
CARS2
RNF219
GRTP1
BORA
TDRD3
DIAPH3
SLITRK6
TMTC4
ABHD13
ZIC5
A2LD1
TEX30
ADPRHL1
SLITRK1
KCTD12
TEX29
METTL21CP1
SLAIN1
PRR20A
SPACA7
RNF113B
LINC00410
HNRNPA1L2
GPR180
COMMD6
CLYBL
METTL21C
TPTE2P3
NALCN
HS6ST3
DAOA
DAOA-AS1
FGF14-IT1
LOC283481
LINC00346
CHAMP1
OR7E156P
UBAC2
LINC00550
LINC00347
FAM70B
C13orf35
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
MZT1
MIR4500HG
FLJ44054
CCDC168
CTAGE11P
FLJ41484
MIR622
MIR623
LINC00460
FAM155A
PRR20B
PRR20C
PRR20D
PRR20E
LINC00552
FKSG29
UBAC2-AS1
MCF2L-AS1
MIR1297
MIR759
MIR4306
MIR3170
MIR3169
MIR3665
RBM26-AS1
LOC100506394
BIVM-ERCC5
MIR2681
MIR548AN
MIR4500
MIR4705

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q21.2.

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

Genes
ALDH2
BCL7A
BTG1
PTPN11
hsa-mir-4304
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
hsa-mir-619
hsa-mir-1827
hsa-mir-4303
hsa-mir-135a-2
hsa-mir-1251
hsa-mir-331
hsa-mir-492
hsa-mir-618
hsa-mir-617
hsa-mir-1252
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
ATP2B1
SCARB1
CMKLR1
COX6A1
CRY1
CSRP2
DAO
DCN
EPYC
DTX1
DUSP6
EIF2B1
ELK3
STX2
GOLGA3
GTF2H3
HAL
HPD
IGF1
KCNC2
LTA4H
LUM
KITLG
MMP17
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
PPP1R12A
NAP1L1
NFYB
NOS1
NTS
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
PAWR
CDK17
SLC25A3
PLA2G1B
PMCH
POLE
PPP1CC
PRKAB1
PSMD9
PXMP2
PXN
RAN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
SNRPF
SYT1
TBX5
TBX3
HNF1A
TDG
TSPAN8
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UBE2N
UNG
ZNF10
ZNF26
ZNF84
ZNF140
ALX1
CDK2AP1
BRAP
ULK1
EEA1
RASAL1
PPFIA2
LGR5
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
GALNT4
CRADD
HRK
ADAM1
LIN7A
SOCS2
HCAR3
HIP1R
RASSF9
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
NR1H4
SH2B3
ARPC3
PLXNC1
MPHOSPH9
CAMKK2
ZNF268
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
GLIPR1
RAB35
SNRNP35
KERA
KRR1
PRDM4
CIT
PWP1
FICD
NUDT4
FZD10
PHLDA1
MLXIP
RPH3A
P2RX2
RAB21
FBXO21
SETD1B
UHRF1BP1L
ANKLE2
CUX2
KIAA1033
MED13L
ZDHHC17
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
MGAT4C
FBXW8
HSPB8
HCAR1
UTP20
MRPL42
IFT81
CCDC59
FAM216A
HCFC2
TRHDE
SYCP3
CHST11
GALNT9
CCDC53
CCDC41
GPN3
GLTP
C12orf47
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
SLC6A15
RIC8B
APPL2
SBNO1
TMEM19
DRAM1
SVOP
STAB2
VEZT
GOLGA2P5
ZCCHC8
SCYL2
POLR3B
CHFR
FGD6
WSB2
NDUFA12
DIABLO
ANKS1B
CHPT1
TMCC3
PITPNM2
EP400
DHX37
FBRSL1
DDX55
NTN4
TRPV4
LHX5
SUDS3
ACTR6
TBC1D15
C12orf43
VPS33A
RSRC2
AACS
NUP37
DDX54
NOC4L
GNPTAB
B3GNT4
TCTN1
ACSS3
OGFOD2
VPS37B
BBS10
C12orf49
TCTN2
NAA25
SLC24A6
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
THAP2
KCTD10
USP44
SLC41A2
LRRIQ1
C12orf26
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
CAPS2
UNC119B
USP30
ORAI1
RNFT2
C12orf34
C12orf52
MGC14436
ANKRD13A
NAV3
TMEM116
UBE3B
C12orf23
C12orf29
C12orf65
TMEM132C
CCDC64
SDSL
TMEM132B
OSBPL8
IQCD
LOC116437
DEPDC4
CCDC38
C12orf45
TMEM132D
SLC15A4
TPH2
NEDD1
SLC9A7P1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
BRI3BP
AMDHD1
GLIPR1L2
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
TSPAN19
E2F7
LOC144481
LOC144486
RAD9B
FAM109A
LOC144742
KRT19P2
TMTC2
TMTC3
C12orf50
ALDH1L2
SLC5A8
PPTC7
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
ZFC3H1
PLBD2
FAM71C
RMST
C12orf12
SLC17A8
GNN
LRRC43
TCP11L2
LOC255480
LOC256021
GLIPR1L1
POC1B
OTOGL
GPR133
MORN3
LOC283392
GAS2L3
LINC00485
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
DDX51
MMAB
HCAR2
LOC338758
TMEM119
LOC338799
C12orf74
EP400NL
RILPL1
PTPRQ
C12orf42
IL31
C12orf75
CCDC42B
TMEM233
SETD8
LOC387895
MKRN9P
C12orf76
LOC400084
FLJ37505
MIR135A2
C12orf37
PLEKHG7
LOC440117
FLJ31485
NUDT4P1
MIR331
EID3
ATXN7L3B
CLLU1OS
CLLU1
MIR492
MAP1LC3B2
LOC643339
LOC643770
LOC647589
SNORA49
SNORA53
MIR617
MIR618
MIR620
LOC728084
C12orf73
LOC728739
MRS2P2
LOC100128191
LOC100128554
LOC100130238
LOC100131138
LOC100131733
LOC100190940
LINC00173
LOC100287944
ZNF605
MIR1252
MIR1827
MIR1178
MIR1251
MIR4303
MIR4304
MIR3685
MIR3612
MIR3652
MIR3922
MIR3908
LOC100505978
LOC100506649
LOC100506668
LOC100507055
LOC100507066
LOC100507091
LOC100507206
LOC100507377
POC1B-GALNT4
ZNF664-FAM101A
MIR4699
MIR4498
MIR548AL
MIR4472-2
MIR4700
MIR4497

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q31.3.

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

Genes
FBXW7
hsa-mir-3140
MIR3140

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q21.23.

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

Genes
MAPK10
ARHGAP24
MIR4451

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q22.3.

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

Genes
BMPR1A
FGFR2
TLX1
NFKB2
PRF1
PTEN
RET
NCOA4
DUX4
SUFU
hsa-mir-202
hsa-mir-378c
hsa-mir-4297
hsa-mir-4296
hsa-mir-2110
hsa-mir-4295
hsa-mir-548e
hsa-mir-609
hsa-mir-936
hsa-mir-1307
hsa-mir-146b
hsa-mir-3158-1
hsa-mir-608
hsa-mir-1287
hsa-mir-607
hsa-mir-3157
hsa-mir-107
hsa-mir-346
hsa-mir-606
hsa-mir-1254
hsa-mir-1296
hsa-mir-548f-1
hsa-mir-605
hsa-mir-4294
hsa-mir-3156-1
ACADSB
ACTA2
ADAM8
ADD3
ADK
ADRA2A
ADRB1
ALOX5
ANXA8L2
ANK3
ANXA2P3
ANXA7
ANXA11
FAS
ARL3
BNIP3
CAMK2G
CASP7
ENTPD1
CDK1
CHAT
CHUK
ABCC2
COL13A1
COL17A1
COX15
CPN1
CTBP2
CTSL1P2
CYP2C19
CYP2C8
CYP2C9
CYP2C18
CYP2E1
CYP17A1
CYP26A1
DMBT1
DNA2
DNTT
DOCK1
DUSP5
ECHS1
EGR2
EIF4EBP2
EMX2
ERCC6
FGF8
GDF2
GDF10
GFRA1
GLUD1
GOT1
PRLHR
GPR26
GRK5
GRID1
HABP2
HELLS
HHEX
HK1
HMX2
HNRNPF
HNRNPH3
HPS1
HTR7
IDE
IFIT2
IFIT1
IFIT3
INPP5A
KCNMA1
KIF11
ABLIM1
LIPA
MAT1A
MBL2
MGMT
MKI67
MSMB
MXI1
NDUFB8
NODAL
NRAP
OAT
P4HA1
PAX2
PCBD1
PDE6C
PGAM1
PITX3
PLAU
PNLIP
PNLIPRP1
PNLIPRP2
PPA1
PPP1R3C
PPP3CB
PPYR1
SRGN
PRKG1
MAPK8
HTRA1
PSAP
PSD
PTPRE
ALDH18A1
RBP3
RBP4
RGR
RGS10
RPS24
SCD
CXCL12
SFRP5
SFTPD
FBXW4
SLC18A2
SLC18A3
SLIT1
SNCG
SUPV3L1
TACR2
TAF5
TCF7L2
TECTB
TFAM
TIAL1
TLL2
UBE2D1
UROS
VCL
VDAC2
WNT8B
XPNPEP1
ZNF22
ZNF32
ZNF33B
CCDC6
SLC25A16
SHOC2
ADAM12
ZNF239
UTF1
PARG
NDST2
MBL1P
LIPF
EIF3A
GBF1
LDB1
SGPL1
BTRC
CH25H
PKD2L1
BTAF1
PAPSS2
INA
PDLIM1
SMC3
NEURL
BUB3
DDX21
LGI1
NOLC1
DLG5
GSTO1
CHST3
BAG3
VPS26A
MINPP1
KIF20B
SEC24C
SH3PXD2A
FAM53B
GPRIN2
SLK
BMS1
SPOCK2
ZNF518A
RHOBTB1
DCLRE1A
FRAT1
PPIF
ACTR1A
HNRNPA3P1
SMNDC1
NPM3
MICU1
GLRX3
RPP30
DPYSL4
TACC2
SORBS1
ERLIN1
LBX1
NRG3
MGEA5
TUBGCP2
PRDX3
C10orf116
VAX1
C10orf10
ATE1
POLR3A
ZWINT
LDB3
SEC23IP
ECD
RAB11FIP2
CPEB3
INPP5F
ZNF365
DKK1
NT5C2
PDCD11
SORCS3
KIAA0913
WAPAL
PPRC1
FAM175B
RRP12
TBC1D12
DNAJC9
DNMBP
CSTF2T
FRAT2
SIRT1
KAT6B
TSPAN15
IFIT5
DPCD
SEC31B
NUDT13
ATRNL1
HERC4
PTPN20B
C10orf137
LRIT1
TCTN3
KIAA1279
C10orf12
ANKRD2
CNNM1
MYOF
DUX2
AP3M1
ANKRD1
GHITM
KIAA1274
PDCD4
VENTX
C10orf28
POLL
CTNNA3
BLNK
A1CF
NRBF2
KCNIP2
CUZD1
CALY
NEUROG3
ASCC1
EXOSC1
MRPS16
CALHM2
CUTC
PLCE1
DUSP13
CHST15
ACSL5
PANK1
FXYD4
FAM190B
EXOC6
FAM35A
DDIT4
CCNJ
MARCH5
ZRANB1
TTC40
NSMCE4A
DNAJB12
CNNM2
C10orf26
C10orf118
CRTAC1
CEP55
LRRC20
CWF19L1
SLC29A3
RNLS
PI4K2A
CSGALNACT2
H2AFY2
HIF1AN
RUFY2
WDR11
FAM178A
FAM21B
CCAR1
OGDHL
DHX32
PPP2R2D
CISD1
FAM45B
TDRD1
DNAJC12
ASAH2
BCCIP
C10orf2
SAR1A
TM9SF3
ENTPD7
ZMIZ1
AS3MT
STAMBPL1
GPAM
KIAA1598
FAM160B1
WDFY4
SEMA4G
ARHGAP22
MYOZ1
PLEKHA1
AVPI1
HPSE2
FAM204A
CDH23
LHPP
PBLD
NPFFR1
C10orf54
MMS19
NOC3L
IKZF5
ZDHHC6
PCDH15
CUEDC2
DDX50
FBXL15
OR13A1
C10orf76
HPS6
MMRN2
TMEM180
MCMBP
SYNPO2L
C10orf95
C10orf81
PDZD7
OBFC1
C10orf88
UBTD1
BICC1
FAM213A
HKDC1
WDR96
TET1
LRRC27
TNKS2
TRIM8
TSPAN14
KAZALD1
SFXN3
SLC25A28
ELOVL3
MARVELD1
SYT15
RASSF4
C10orf11
PCGF6
ARID5B
LOXL4
ZDHHC16
C10orf58
DYDC2
PCGF5
GPR123
LZTS2
PHYHIPL
LCOR
NKX6-2
MRPL43
AFAP1L2
PLA2G12B
MYPN
PYROXD2
USMG5
LOC84856
ZNF503
AIFM2
ADO
ATAD1
ARHGAP19
LOC84989
KNDC1
ITPRIP
LINC00263
MCU
MTG1
CDHR1
BBIP1
FANK1
OPALIN
SYCE1
ZFAND4
OPN4
HOGA1
SORCS1
C10orf71
PRAP1
ZNF511
CHCHD1
ZMYND17
TTC18
C10orf90
BTBD16
FAM24A
PSTK
ZNF488
PIK3AP1
MORN4
ZFYVE27
MMP21
COMTD1
FRA10AC1
ANKRD22
SFXN2
PDZD8
AGAP4
C10orf32
NUDT9P1
AGAP11
GSTO2
SFR1
CALHM3
CTAGE7P
CLRN3
ANAPC16
PNLIPRP3
SFXN4
CPXM2
ADAMTS14
C10orf129
SAMD8
LIPJ
CFL1P1
TRUB1
FRMPD2
VTI1A
LOC143188
DYDC1
EIF5AL1
HECTD2
FGFBP3
C10orf82
C10orf46
USP54
NKX2-3
SLC35G1
CCDC147
FAM170B
C10orf128
FUT11
OIT3
C10orf91
PWWP2B
LOC170425
ANTXRL
EMX2OS
PPAPDC1A
VSTM4
PAOX
FAM24B
LOC219347
PLAC9
C10orf107
TMEM26
ZCCHC24
UNC5B
STOX1
C10orf35
TYSND1
RTKN2
C10orf27
ATOH7
SLC16A9
FAM13C
MARCH8
C10orf25
TMEM72-AS1
ZNF485
RASGEF1A
REEP3
JMJD1C
ZNF503-AS1
IPMK
FAM21C
EBF3
CALHM1
CASC2
TCERG1L
HSPA12A
SGMS1
PIPSL
PGBD3
C10orf53
C10orf125
JAKMIP3
STK32C
BLOC1S2
RBM20
LOC282997
FLJ37201
C10orf40
LOC283033
LOC283038
LOC283050
LOC283089
FAM149B1
FLJ31813
O3FAR1
KCNK18
LOC338579
DUPD1
LIPM
CYP26C1
VWA2
NANOS1
LRIT2
HMX3
LRRTM3
NHLRC2
C10orf96
FLJ46361
FAM21A
SH2D4B
C10orf99
SLC16A12
CC2D2B
ENO4
ARMS2
C10orf122
LOC387723
GUCY2GP
NKX1-2
LOC399753
BMS1P5
FLJ41350
C10orf120
LOC399815
METTL10
FLJ37035
FOXI2
FLJ46300
LOC399829
SPRNP1
GOLGA7B
FAM45A
MIR107
C10orf105
C10orf62
AGAP6
ZNF32-AS3
C10orf55
FAM35B
C10orf103
C10orf136
FAM35B2
LOC439990
LOC439994
IFIT1B
FRG2B
LOC441666
MIR346
LRRC18
SPRN
MIR146B
MIR202
NPS
LOC619207
SNORA19
LOC642361
AGAP9
ZNF487P
LOC642826
FAM196A
FAM25A
TMEM72
LIPK
LIPN
LOC643529
LOC643650
FAM25C
DRGX
RPL13AP6
LOC650623
PTPN20A
ANXA8
AGAP7
ASAH2B
SFTPA1
DUX4L7
DUX4L6
DUX4L5
DUX4L3
SNORA12
SNORD98
MIR605
MIR608
MIR609
BMS1P1
ANXA8L1
FAM22A
FAM22D
LOC728190
LOC728218
AGAP8
LOC728407
DUX4L2
LOC728558
LOC728640
LOC728643
FRMPD2P1
LOC728978
LOC729020
AGAP5
BMS1P4
SFTPA2
TLX1NB
MIR936
C10orf131
LOC100128054
LOC100128292
ZNF37BP
ZNF503-AS2
FAM25B
LOC100132987
FAM25G
LOC100133308
KLLN
LOC100169752
LOC100188947
DNMBP-AS1
TIMM23
LOC100288974
LOC100289509
MIR1287
MIR1296
MIR1256
MIR1307
MIR2110
FAS-AS1
MIR378C
MIR4297
MIR3157
MIR4294
MIR3158-1
MIR4295
MIR3156-1
MIR3158-2
MIR4296
MTRNR2L5
MIR3924
MIR3941
MIR3663
MIR3944
LOC100505540
LOC100505761
LOC100505839
LOC100505933
LOC100506733
LOC100506835
LOC100506939
M1
LOC100507331
LOC100507470
MARK2P9
C10orf32-AS3MT
ARHGAP19-SLIT1
FAM24B-CUZD1
MIR4680
MIR4679-1
MIR4483
MIR4679-2
MIR4676
MIR4678
MIR4682
MIR4482-1
MIR4484
MIR4681
MIR4685

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q31.1.

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

Genes
AKT1
KTN1
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
TCL6
BCL11B
hsa-mir-203
hsa-mir-4309
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-345
hsa-mir-342
hsa-mir-3173
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
hsa-mir-4308
SERPINA3
ACTN1
ACYP1
ARG2
BDKRB1
BDKRB2
BMP4
ZFP36L1
CALM1
SERPINA6
ENTPD5
CDKN3
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EIF5
ELK2AP
EML1
ERH
ESR2
ESRRB
FNTB
FOS
FUT8
GALC
GCH1
GMFB
GPX2
GSTZ1
GTF2A1
BRF1
HIF1A
HSPA2
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
LGALS3
LTBP2
MARK3
MAX
ATXN3
MAP3K9
ALDH6A1
MNAT1
MTHFD1
NDUFB1
SIX6
OTX2
SERPINA5
PGF
SERPINA1
SERPINA4
PIGH
PPM1A
PPP2R5C
PPP2R5E
PRKCH
LGMN
PSEN1
PSMA3
PSMC1
ABCD4
RAD51B
MOK
ARID4A
RTN1
SEL1L
SRSF5
SIX1
SLC8A3
SLC10A1
SNAPC1
SPTB
TGFB3
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
ZBTB25
DPF3
GPR68
GPR65
NUMB
ADAM21
ADAM20
ADAM6
DLK1
CCNK
DCAF5
ALKBH1
EIF2B2
MTA1
PNMA1
RPS6KA5
NRXN3
AKAP5
SPTLC2
BAG5
C14orf2
CDC42BPB
TCL1B
RGS6
KIAA0247
KIAA0586
DLGAP5
KIAA0125
KIAA0317
TECPR2
MED6
CNIH
VTI1B
FBLN5
BATF
SIVA1
NPC2
AHSA1
EXOC5
CGRRF1
CYP46A1
PAPOLA
ACOT2
TMED10
PTPN21
C14orf1
WDHD1
VASH1
ATG14
ZBTB1
SNW1
PCNX
DAAM1
SAMD4A
TTLL5
RCOR1
SYNE2
PACS2
ANGEL1
PPP1R13B
ZFYVE26
TTC9
FLRT2
PLEKHG3
SIPA1L1
DCAF4
KIF26A
C14orf109
PLEK2
TIMM9
MLH3
KCNH5
PRO1768
GPR132
POMT2
COQ6
FCF1
RDH11
SERPINA10
GLRX5
COX16
DACT1
ATP6V1D
EVL
C14orf129
JKAMP
CINP
DHRS7
ASB2
SIX4
ZFYVE1
CPSF2
KCNK10
C14orf101
FBXO34
CDCA4
C14orf102
ATG2B
UBR7
C14orf105
EXD2
VRTN
SYNJ2BP
SLC39A9
MEG3
FLVCR2
C14orf118
SMEK1
BTBD7
MUDENG
TDP1
ZNF839
SPATA7
ACTR10
YLPM1
KCNK13
C14orf162
C14orf132
DDX24
ADCK1
TMEM63C
PELI2
RHOJ
GALNTL1
PLEKHH1
TRMT5
UNC79
BEGAIN
PPP4R4
ZNF410
NGB
RBM25
C14orf133
SMOC1
MOAP1
DIO3OS
IRF2BPL
MPP5
INF2
C14orf135
GPR135
OTUB2
ZFYVE21
MEG8
WDR25
LINC00341
ZC2HC1C
C14orf169
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
C14orf45
TMEM121
SGPP1
AMN
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
STON2
KIAA1737
PAPLN
FAM181A
BTBD6
EFCAB11
CHURC1
C14orf43
LIN52
NEK9
EXOC3L4
WDR20
MAPK1IP1L
IFT43
WDR89
C14orf149
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
SOCS4
NAA30
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
LINC00239
LOC145216
RDH12
ADAM21P1
GSC
SERPINA12
PRIMA1
PPP1R36
SLC38A6
C14orf37
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
TTC7B
FAM71D
TMEM229B
C14orf49
TMEM30B
SAMD15
EML5
MGC23270
NUDT14
LINC00521
SERPINA11
PROX2
ZDHHC22
TMED8
C14orf178
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
KIAA0284
C14orf80
C14orf55
C14orf39
CCDC85C
ITPK1-AS1
SNORD56B
SERPINA9
LINC00226
LINC00221
VSX2
SLC35F4
COX8C
ASPG
RAB15
FLJ31306
TBPL2
TOMM20L
SERPINA13
C14orf64
RTL1
TMEM179
HEATR4
FLJ22447
PLEKHD1
LOC400236
LOC400238
DICER1-AS1
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
LINC00238
CCDC88C
TEX21P
MIR323A
MIR337
MIR345
MIR376C
MIR369
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR323B
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
LOC645431
RPL13AP3
LINC00520
FLJ43390
SYNDIG1L
TEX22
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
SNORA79
MIR411
MIR654
MIR655
MIR656
C14orf38
LOC731223
SNORD113-1
SNORD113-2
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
KTN1-AS1
LOC100129345
LOC100131366
LOC100289511
MIR1247
MIR1185-1
MIR1185-2
MIR1260A
MIR1197
OTX2OS1
MIR1193
MIR4309
MIR3173
MIR4308
LOC100506321
LOC100507043
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR3545
MIR4708
MIR4709
MIR4710
MIR4706
MIR2392
LOC100628307
HIF1A-AS2

Arm-level results

Table 3. Get Full Table Arm-level significance table - 24 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	2121	0.20	-0.496	1	0.27	1.37	0.216
1q	1955	0.36	2.92	0.0115	0.22	-0.428	1
2p	924	0.39	0.887	0.75	0.10	-4.7	1
2q	1556	0.31	0.618	0.976	0.16	-2.5	1
3p	1062	0.23	-1.6	1	0.65	7.1	2.58e-11
3q	1139	0.44	2.45	0.0411	0.35	0.44	0.574
4p	489	0.22	-2.66	1	0.63	5.06	2.85e-06
4q	1049	0.16	-3.06	1	0.53	4.5	1.9e-05
5p	270	0.51	1.64	0.224	0.49	1.17	0.271
5q	1427	0.17	-2.2	1	0.50	4.82	7.36e-06
6p	1173	0.24	-1.75	1	0.29	-0.687	1
6q	839	0.19	-3.47	1	0.29	-1.59	1
7p	641	0.60	4.7	2.66e-05	0.24	-2.3	1
7q	1277	0.50	4.43	4.61e-05	0.19	-2.2	1
8p	580	0.49	1.9	0.143	0.54	2.88	0.00712
8q	859	0.58	4.89	1.99e-05	0.26	-1.64	1
9p	422	0.17	-3.6	1	0.62	4.58	1.51e-05
9q	1113	0.26	-1.23	1	0.47	3.11	0.00414
10p	409	0.24	-3.24	1	0.36	-0.973	1
10q	1268	0.18	-2.64	1	0.35	0.751	0.453
11p	862	0.28	-1.45	1	0.40	0.93	0.371
11q	1515	0.25	-0.619	1	0.44	3.62	0.000726
12p	575	0.41	0.411	1	0.25	-2.56	1
12q	1447	0.23	-1.49	1	0.20	-2.13	1
13q	654	0.36	-0.288	1	0.53	2.95	0.0063
14q	1341	0.33	0.542	0.98	0.34	0.694	0.465
15q	1355	0.25	-1.1	1	0.33	0.609	0.493
16p	872	0.28	-1.56	1	0.36	-0.00512	0.837
16q	702	0.25	-2.42	1	0.34	-0.753	1
17p	683	0.24	-2.39	1	0.48	2.22	0.0439
17q	1592	0.26	-0.33	1	0.19	-1.82	1
18p	143	0.38	-0.958	1	0.50	1.22	0.264
18q	446	0.20	-3.09	1	0.62	4.65	1.31e-05
19p	995	0.15	-3.63	1	0.40	1.36	0.216
19q	1709	0.18	-1.67	1	0.35	2.19	0.0444
20p	355	0.58	3.36	0.00311	0.31	-1.75	1
20q	753	0.57	4.54	3.76e-05	0.15	-3.46	1
21q	509	0.21	-2.82	1	0.63	5.2	1.97e-06
22q	921	0.28	-1.27	1	0.44	1.82	0.0977
Xq	1312	0.28	-0.619	1	0.29	-0.311	0.995

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/ESCA-TP/9824934/GDAC_MergeDataFiles_9194541/ESCA-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_with_miR_20120227.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 126 Input Tumor Samples.

Tumor Sample Names
TCGA-IC-A6RE-01A-11D-A33D-01
TCGA-IC-A6RF-01A-13D-A33D-01
TCGA-IG-A3I8-01A-11D-A246-01
TCGA-IG-A3QL-01A-11D-A246-01
TCGA-IG-A3Y9-01A-12D-A246-01
TCGA-IG-A3YA-01A-11D-A246-01
TCGA-IG-A3YB-01A-11D-A246-01
TCGA-IG-A3YC-01A-11D-A246-01
TCGA-IG-A4P3-01A-11D-A25X-01
TCGA-IG-A4QS-01A-11D-A25X-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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