Ovarian Serous Cystadenocarcinoma: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
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 2.0.16 (cga svn revision 38839).

Summary

There were 558 tumor samples used in this analysis: 29 significant arm-level results, 34 significant focal amplifications, and 47 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 - 34 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
--- | --- | --- | --- | ---
8q24.21 | 1.2697e-95 | 1.2697e-95 | chr8:128878025-129309687 | 8
19q12 | 6.8108e-102 | 9.8837e-90 | chr19:30307452-30312349 | 1
3q26.2 | 2.2398e-72 | 2.2398e-72 | chr3:168670631-168790486 | 0 [MECOM]
1p34.3 | 6.1251e-28 | 6.1251e-28 | chr1:39439539-41469843 | 37
11q14.1 | 1.6969e-27 | 1.6969e-27 | chr11:77620713-78079501 | 9
19p13.12 | 4.4781e-26 | 4.4781e-26 | chr19:15333311-15400860 | 2
12p12.1 | 1.7461e-25 | 6.7418e-22 | chr12:25362516-25370699 | 1
1q21.3 | 1.5887e-20 | 1.5471e-17 | chr1:150516762-150739128 | 8
19q13.2 | 3.527e-26 | 4.1175e-09 | chr19:40040784-40406796 | 10
14q11.2 | 8.3812e-10 | 1.3042e-08 | chr14:21338460-21606746 | 13
7q36.1 | 1.8677e-08 | 1.8677e-08 | chr7:145566533-159138663 | 110
20q13.33 | 2.0141e-08 | 1.197e-07 | chr20:60781395-61420277 | 18
15q26.3 | 5.1943e-07 | 5.1943e-07 | chr15:97368383-102531392 | 35
1q42.3 | 8.3812e-10 | 5.6932e-07 | chr1:234420230-235770716 | 17
18q11.2 | 4.8194e-06 | 4.8194e-06 | chr18:23857484-24293308 | 3
5p15.33 | 4.9232e-06 | 4.9232e-06 | chr5:1-1350010 | 25
20q11.21 | 1.4144e-06 | 1.0714e-05 | chr20:30167682-30332464 | 6
4p16.3 | 1.1149e-05 | 1.1149e-05 | chr4:1733551-1817843 | 3
6p22.3 | 2.2916e-06 | 1.6194e-05 | chr6:18461159-18506750 | 1
4q13.3 | 1.6549e-05 | 1.6549e-05 | chr4:73812807-74192807 | 2
10q22.3 | 1.8331e-05 | 1.8331e-05 | chr10:79307097-79800033 | 5
2q31.2 | 3.3336e-05 | 3.3336e-05 | chr2:176832038-178859742 | 29
8p11.21 | 6.8559e-05 | 6.8559e-05 | chr8:41533339-42211770 | 6
22q12.2 | 7.5599e-05 | 7.5599e-05 | chr22:30113489-30316638 | 5
12q15 | 6.2087e-05 | 0.001062 | chr12:69692167-71082271 | 13
12p13.33 | 1.2589e-05 | 0.0011419 | chr12:1-4462597 | 39
17q25.3 | 0.0029794 | 0.0029794 | chr17:80234896-80283879 | 2
14q32.33 | 0.00011668 | 0.0056912 | chr14:105140737-107349540 | 29
10p15.3 | 0.0076124 | 0.0076124 | chr10:646802-1426759 | 10
2p23.2 | 0.061354 | 0.061354 | chr2:28811078-28954584 | 1
6q21 | 0.08164 | 0.08164 | chr6:106967186-107324217 | 5
11p13 | 0.087045 | 0.087045 | chr11:32246347-32707914 | 4
12q13.11 | 0.006065 | 0.21397 | chr12:45856454-46994005 | 5
6p21.1 | 0.053617 | 0.23478 | chr6:36692241-44540981 | 117

Genes in Wide Peak

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

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

Genes
hsa-mir-1208
hsa-mir-1207
hsa-mir-1205
PVT1
MIR1205
MIR1206
MIR1207
MIR1208

Genes in Wide Peak

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

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

Genes
CCNE1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p34.3.

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

Genes
MYCL1
hsa-mir-30c-1
BMP8B
COL9A2
CTPS
NDUFS5
NFYC
PPT1
RLF
PABPC4
KCNQ4
RIMS3
ZMPSTE24
PPIE
CAP1
MACF1
HEYL
HPCAL4
TRIT1
OXCT2
SMAP2
DEM1
ZNF643
AKIRIN1
NT5C1A
MFSD2A
TMCO2
ZNF684
CITED4
ZNF642
BMP8A
MIR30C1
MIR30E
KIAA0754
SNORA55
PPIEL
LOC100130557

Genes in Wide Peak

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

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

Genes
NDUFC2
THRSP
GAB2
USP35
KCTD14
ALG8
INTS4
KCTD21
NDUFC2-KCTD14

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19p13.12.

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

Genes
BRD4
EPHX3

Genes in Wide Peak

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

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

Genes
KRAS

Genes in Wide Peak

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

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

Genes
hsa-mir-4257
CTSS
ENSA
MCL1
ADAMTSL4
GOLPH3L
HORMAD1
MIR4257

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.2.

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

Genes
CLC
FBL
FCGBP
DYRK1B
LGALS13
LGALS14
LGALS16
LEUTX
LGALS17A
LOC100129935

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q11.2.

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

Genes
RNASE2
RNASE3
SLC39A2
ZNF219
ARHGEF40
NDRG2
METTL17
RNASE7
TPPP2
RNASE8
RNASE13
ECRP
C14orf176

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q36.1.

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

Genes
EZH2
MLL3
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
ABP1
CDK5
DPP6
EN2
GBX1
MNX1
HTR5A
INSIG1
KCNH2
NOS3
PTPRN2
RARRES2
RHEB
SHH
SLC4A2
SMARCD3
VIPR2
XRCC2
ZNF212
ZNF282
CUL1
ACCN3
PDIA4
UBE3C
DNAJB6
ABCF2
FASTK
ABCB8
PAXIP1
SSPO
CNTNAP2
GIMAP2
ZNF777
TMEM176B
REPIN1
PRKAG2
NUB1
CHPF2
NCAPG2
WDR60
GIMAP4
GIMAP5
TMEM176A
ACTR3B
ESYT2
ZNF398
GALNT11
LMBR1
LINC00244
NOM1
LRRC61
ZNF767
TMUB1
KRBA1
C7orf29
AGAP3
C7orf13
ZNF786
ASB10
RNF32
LOC154822
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
GALNTL5
GIMAP7
ZNF467
GIMAP1
LOC202781
C7orf33
FABP5P3
CNPY1
LOC285889
ZNF775
LOC285972
ATG9B
WDR86
LOC401431
MIR153-2
GIMAP6
ZNF862
LOC645249
ACTR3C
MIR595
LOC728743
MIR671
LOC100128264
LOC100128822
LOC100131176
LOC100132707
ZNF783
MIR548F3
MIR548I4
MIR548F4
MIR548T
MIR3907
LOC100505483
LOC100506585
GIMAP1-GIMAP5

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.33.

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

Genes
hsa-mir-133a-2
LAMA5
NTSR1
RPS21
OSBPL2
ADRM1
HRH3
SLCO4A1
CABLES2
C20orf166
GATA5
C20orf151
C20orf166-AS1
MIR1-1
MIR133A2
LOC100127888
MIR4758
LOC100652730

Genes in Wide Peak

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

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

Genes
hsa-mir-1302-10
ALDH1A3
IGF1R
MEF2A
PCSK6
SNRPA1
CHSY1
SYNM
OR4F4
LINS
SELS
TTC23
LRRK1
TM2D3
ARRDC4
LOC91948
TARSL2
LRRC28
ASB7
LYSMD4
PGPEP1L
ADAMTS17
DNM1P46
CERS3
FAM169B
WASH3P
FLJ42289
OR4F6
OR4F15
FAM138E
GPCRLTM7
DDX11L1
DDX11L9
LOC100507472
MIR4714

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q42.3.

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

Genes
GNG4
TARBP1
TBCE
GGPS1
TOMM20
RBM34
ARID4B
SLC35F3
B3GALNT2
IRF2BP2
C1orf31
SNORA14B
LINC00184
LOC100506795
LOC100506810
MIR4753
MIR4671

Genes in Wide Peak

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

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

Genes
TAF4B
KCTD1
LOC728606

Genes in Wide Peak

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

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

Genes
SDHA
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
PP7080
CEP72
AHRR
BRD9
ZDHHC11
CLPTM1L
NKD2
C5orf55
CCDC127
PLEKHG4B
SLC6A19
SLC6A18
LRRC14B
LOC100506688
MIR4457
MIR4456
MIR4635

Genes in Wide Peak

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

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

Genes
hsa-mir-3193
BCL2L1
ID1
TPX2
COX4I2
MIR3193

Genes in Wide Peak

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

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

Genes
FGFR3
LETM1
TACC3

Genes in Wide Peak

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

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

Genes
RNF144B

Genes in Wide Peak

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

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

Genes
ANKRD17
COX18

Genes in Wide Peak

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

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

Genes
KCNMA1
RPS24
DLG5
POLR3A
LOC100128292

Genes in Wide Peak

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

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

Genes
HOXD11
HOXD13
NFE2L2
hsa-mir-3128
hsa-mir-1246
hsa-mir-10b
HOXD1
HOXD3
HOXD4
HOXD8
HOXD9
HOXD10
HOXD12
AGPS
MTX2
PDE11A
KIAA1715
TTC30A
TTC30B
HNRNPA3
EVX2
LOC375295
LOC401022
MIR10B
LOC100130691
MIR1246
MIR3128
LOC100506783
MIR4444-1

Genes in Wide Peak

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

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

Genes
ANK1
IKBKB
PLAT
POLB
KAT6A
AP3M2

Genes in Wide Peak

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

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

Genes
MTMR3
UQCR10
ZMAT5
ASCC2
CABP7

Genes in Wide Peak

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

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

Genes
LYZ
CNOT2
PTPRB
PTPRR
YEATS4
CCT2
FRS2
KCNMB4
RAB3IP
BEST3
LRRC10
MIR3913-2
MIR3913-1

Genes in Wide Peak

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

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

Genes
CCND2
KDM5A
CACNA1C
FKBP4
FOXM1
NINJ2
RAD52
SLC6A12
SLC6A13
TEAD4
TULP3
TSPAN9
ERC1
ITFG2
PRMT8
PARP11
C12orf5
WNK1
ADIPOR2
WNT5B
C12orf32
NRIP2
CCDC77
EFCAB4B
CACNA2D4
FBXL14
DCP1B
B4GALNT3
LOC283440
IQSEC3
LOC574538
LRTM2
FAM138D
LOC100271702
LOC100288778
LOC100292680
MIR3649
LOC100507424
LOC100652846

Genes in Wide Peak

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

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

Genes
CD7
SECTM1

Genes in Wide Peak

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

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

Genes
AKT1
CRIP1
CRIP2
ELK2AP
BRF1
JAG2
ADAM6
MTA1
KIAA0125
SIVA1
PACS2
GPR132
CDCA4
INF2
TMEM121
BTBD6
AHNAK2
C14orf79
PLD4
ADSSL1
MGC23270
NUDT14
KIAA0284
C14orf80
LINC00226
LINC00221
TEX22
ZBTB42
MIR4710

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10p15.3.

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

Genes
ADARB2
IDI1
WDR37
DIP2C
LARP4B
GTPBP4
IDI2-AS1
IDI2
LINC00200
C10orf108

Genes in Wide Peak

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

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

Genes
PLB1

Genes in Wide Peak

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

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

Genes
hsa-mir-587
AIM1
QRSL1
RTN4IP1
LOC100422737

Genes in Wide Peak

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

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

Genes
WT1
EIF3M
WT1-AS
CCDC73

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q13.11.

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

Genes
SCAF11
SLC38A2
SLC38A1
ARID2
LOC400027

Genes in Wide Peak

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

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

Genes
CCND3
PIM1
TFEB
BYSL
CDC5L
DNAH8
SLC29A1
GLO1
GLP1R
GUCA1A
GUCA1B
HSP90AB1
MDFI
MEA1
MOCS1
NFKBIE
NFYA
PEX6
PGC
POLH
PPP2R5D
PTK7
PRPH2
SRF
TBCC
VEGFA
KCNK5
RNF8
NCR2
MED20
POLR1C
MAD2L1BP
CUL7
C6orf108
CNPY3
FRS3
SLC22A7
APOBEC2
CAPN11
FTSJD2
CUL9
UBR2
DAAM2
KIAA0240
MTCH1
ZNF318
YIPF3
USP49
GNMT
PRICKLE4
MRPL2
PPIL1
TREM2
TREM1
GTPBP2
MRPS18A
MRPS10
TMEM63B
TBC1D22B
SAYSD1
TRERF1
LRFN2
AARS2
XPO5
CPNE5
ZFAND3
MRPL14
DLK2
TREML2
KCNK16
TTBK1
RRP36
KCNK17
ABCC10
KLC4
TJAP1
BTBD9
FOXP4
KLHDC3
TAF8
CCDC167
PTCRA
TCTE1
SPATS1
C6orf223
RSPH9
LRRC73
TREML2P1
LOC221442
C6orf130
KIF6
TMEM217
FGD2
PI16
C6orf89
TSPO2
UNC5CL
MDGA1
TREML4
RPL7L1
TREML1
TREML3
SLC35B2
FLJ41649
CRIP3
C6orf226
TMEM151B
ATP6V0CP3
C6orf132
TDRG1
LOC100131047
LOC100132354
TOMM6
MIR4647
MIR4641
MIR4642
MIR4462

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

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
19p13.3 | 6.9662e-120 | 3.5784e-91 | chr19:1-1867911 | 77
22q13.32 | 6.533e-48 | 6.533e-48 | chr22:48026910-51304566 | 46
13q14.2 | 4.9843e-41 | 3.0338e-37 | chr13:48833767-48992809 | 1
5q11.2 | 1.5032e-63 | 2.5757e-33 | chr5:58145167-59787985 | 3
11p15.5 | 1.4442e-27 | 1.424e-27 | chr11:1-748945 | 36
6q27 | 1.867e-27 | 1.8699e-27 | chr6:161693099-171115067 | 50
15q15.1 | 3.1512e-27 | 3.1512e-27 | chr15:41832910-42068054 | 4
1p36.11 | 1.6991e-42 | 1.2538e-26 | chr1:26752993-27570286 | 17
7p22.1 | 8.1339e-25 | 8.1339e-25 | chr7:1-6369376 | 73
4q34.3 | 9.397e-29 | 6.408e-24 | chr4:178911874-183060693 | 1
17q11.2 | 7.3817e-20 | 7.4211e-20 | chr17:29326736-29722618 | 5
18q23 | 5.4629e-17 | 5.3346e-17 | chr18:67995567-78077248 | 36
2q22.1 | 3.6141e-19 | 3.89e-16 | chr2:139655617-143637838 | 1
8p23.3 | 8.518e-22 | 3.0131e-15 | chr8:1-1459231 | 7
10q23.31 | 4.7051e-16 | 2.0258e-13 | chr10:89604733-90034038 | 2
4q22.1 | 1.386e-13 | 3.2309e-10 | chr4:90844993-93240505 | 1
2q37.3 | 3.652e-13 | 3.9696e-09 | chr2:235913227-243199373 | 80
5q13.2 | 1.7652e-65 | 4.1813e-09 | chr5:66492413-77299645 | 73
16q23.1 | 1.0031e-14 | 3.3557e-07 | chr16:78016120-79627770 | 2
8p21.2 | 3.1289e-11 | 1.4887e-06 | chr8:25896447-26250295 | 1
9q34.13 | 1.8297e-06 | 1.8147e-06 | chr9:132395508-140219854 | 179
14q23.3 | 2.6572e-06 | 2.6131e-06 | chr14:62262526-73138188 | 78
3p26.3 | 4.1059e-07 | 8.4975e-06 | chr3:1-6903296 | 16
16p13.3 | 1.3843e-05 | 1.3868e-05 | chr16:3764793-4013466 | 1
12q24.33 | 1.1108e-08 | 0.00011546 | chr12:131692956-133851895 | 27
19q13.43 | 1.2519e-07 | 0.00011926 | chr19:58368882-59128983 | 35
10q26.3 | 7.7522e-07 | 0.00017132 | chr10:129922812-135534747 | 52
12q23.1 | 4.5456e-07 | 0.00020164 | chr12:99124001-100431272 | 2
3p21.1 | 5.7128e-05 | 0.0018697 | chr3:48369598-61547330 | 191
5q14.3 | 1.4101e-42 | 0.0018697 | chr5:73105276-106712758 | 134
11q25 | 0.0019594 | 0.0019303 | chr11:126875846-135006516 | 35
21q11.2 | 0.0022643 | 0.0025077 | chr21:1-17913227 | 27
19p13.3 | 3.3019e-87 | 0.0029248 | chr19:1103802-4821598 | 132
2p25.3 | 0.0049448 | 0.0049448 | chr2:1-24166660 | 104
1q32.3 | 0.0053254 | 0.0054006 | chr1:207316102-220046617 | 72
1p36.23 | 1.1863e-23 | 0.0056221 | chr1:1-24383499 | 381
21q22.3 | 0.0073147 | 0.0089603 | chr21:42519390-48129895 | 103
16q22.1 | 6.4762e-06 | 0.012797 | chr16:68479657-68879824 | 3
9p24.3 | 0.016211 | 0.01607 | chr9:1-7797965 | 46
16q24.3 | 1.289e-10 | 0.019177 | chr16:88525832-90354753 | 49
19q13.32 | 1.56e-06 | 0.019177 | chr19:45384488-49318238 | 161
13q11 | 3.3746e-06 | 0.041846 | chr13:1-24043829 | 30
6p25.3 | 0.04517 | 0.044643 | chr6:1-2624052 | 10
1p31.1 | 0.0011525 | 0.12835 | chr1:63777022-118406643 | 365
10p15.3 | 0.14263 | 0.14238 | chr10:1-4693335 | 19
17p12 | 0.15945 | 0.15833 | chr17:11896630-12456081 | 3
3q13.31 | 0.17491 | 0.17518 | chr3:116161663-118620828 | 1

Genes in Wide Peak

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

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

Genes
STK11
TCF3
FSTL3
hsa-mir-1909
hsa-mir-3187
hsa-mir-1302-11
ATP5D
AZU1
HCN2
BSG
CDC34
CIRBP
CNN2
CFD
ARID3A
EFNA2
ELANE
GAMT
GPX4
GZMM
PALM
POLR2E
POLRMT
PRTN3
PTBP1
RPS15
MADCAM1
PPAP2C
MED16
APC2
ABCA7
UQCR11
SBNO2
HMHA1
SHC2
DAZAP1
FGF22
THEG
MBD3
MIER2
PCSK4
C19orf24
RNF126
WDR18
REXO1
LPPR3
OR4F17
KLF16
KISS1R
MUM1
MIDN
R3HDM4
C19orf6
TPGS1
REEP6
GRIN3B
C19orf21
PLK5
C2CD4C
CIRBP-AS1
C19orf25
ATP8B3
C19orf26
ODF3L2
ADAMTSL5
NDUFS7
WASH5P
ONECUT3
MEX3D
FLJ45445
PRSS57
FAM138F
FAM138A
LOC100288123
MIR1909
MIR3187
MIR4745

Genes in Wide Peak

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

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

Genes
hsa-mir-3201
ACR
ARSA
CHKB
CPT1B
TYMP
MAPK11
MAPK12
SBF1
PPP6R2
ZBED4
SCO2
RABL2B
MLC1
MAPK8IP2
PLXNB2
BRD1
FAM19A5
NCAPH2
MOV10L1
MIOX
PANX2
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
SHANK3
TUBGCP6
LOC90834
LMF2
KLHDC7B
LOC284933
RPL23AP82
C22orf34
CHKB-CPT1B
IL17REL
FAM116B
PIM3
ODF3B
SYCE3
LOC100128946
LOC100144603
MIR3201
MIR4535

Genes in Wide Peak

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

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

Genes
LPAR6

Genes in Wide Peak

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

Table S37. Genes in bold are cancer genes as defined by The Sanger Institute's 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 11p15.5.

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

Genes
HRAS
hsa-mir-210
DRD4
IRF7
PSMD13
RNH1
SCT
RASSF7
IFITM1
IFITM3
DEAF1
IFITM2
PKP3
SIRT3
BET1L
CDHR5
PHRF1
SIGIRR
RIC8A
EPS8L2
ATHL1
PTDSS2
ODF3
LRRC56
LOC143666
SCGB1C1
NLRP6
C11orf35
TMEM80
ANO9
B4GALNT4
IFITM5
MIR210
LOC653486
LOC100133161
MIR210HG

Genes in Wide Peak

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

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

Genes
MLLT4
FGFR1OP
hsa-mir-1913
CCR6
GPR31
KIF25
PARK2
PDCD2
PSMB1
RPS6KA2
T
TBP
TCP10
TCTE3
THBS2
RNASET2
QKI
PDE10A
C6orf123
DLL1
BRP44L
UNC93A
PHF10
C6orf70
SMOC2
FRMD1
C6orf208
TTLL2
FAM120B
LINC00473
SFT2D1
PACRG
LOC154449
DACT2
C6orf118
WDR27
LOC285796
PRR18
C6orf120
DKFZp451B082
TCP10L2
LINC00242
LOC441177
MLLT4-AS1
HGC6.3
LOC100289495
MIR1913
MIR3939
CAHM
MIR4644

Genes in Wide Peak

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

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

Genes
hsa-mir-626
TYRO3
MGA
MIR626

Genes in Wide Peak

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

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

Genes
ARID1A
hsa-mir-1976
SFN
HMGN2
RPS6KA1
SLC9A1
NR0B2
NUDC
GPN2
PIGV
GPATCH3
DHDDS
ZDHHC18
FAM46B
C1orf172
TRNP1
MIR1976

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7p22.1.

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

Genes
PMS2
CARD11
hsa-mir-589
hsa-mir-339
ACTB
GNA12
GPER
LFNG
NUDT1
PDGFA
PRKAR1B
FSCN1
AIMP2
MAFK
MAD1L1
EIF3B
CYTH3
KIAA0415
ADAP1
IQCE
SUN1
WIPI2
INTS1
EIF2AK1
SNX8
FTSJ2
GET4
CCZ1
RNF216
CYP2W1
HEATR2
CHST12
RADIL
PAPOLB
FAM20C
RBAK
MICALL2
FBXL18
TTYH3
USP42
PSMG3
C7orf50
TNRC18
ZFAND2A
COX19
KIAA1908
GPR146
AMZ1
TMEM184A
BRAT1
SDK1
FOXK1
MMD2
SLC29A4
RSPH10B
TFAMP1
UNCX
LOC389458
ELFN1
ZNF815
RNF216P1
FLJ44511
LOC442497
MIR339
ZNF890P
OCM
MIR589
RSPH10B2
LOC100288524
RBAK-LOC389458
MIR4648
MIR4655
MIR4656

Genes in Wide Peak

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

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

Genes
LINC00290

Genes in Wide Peak

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

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

Genes
NF1
EVI2A
EVI2B
OMG
MIR4733

Genes in Wide Peak

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

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

Genes
CYB5A
GALR1
MBP
NFATC1
ZNF236
CTDP1
ZNF516
TSHZ1
TXNL4A
ADNP2
KCNG2
SALL3
TIMM21
ZNF407
CNDP2
RBFA
PQLC1
NETO1
PARD6G
CNDP1
FAM69C
CBLN2
FBXO15
ZADH2
C18orf62
LOC284276
LOC339298
ATP9B
LOC400655
LOC400657
HSBP1L1
C18orf63
LOC100130522
LOC100131655
LOC100505776
LOC100505817

Genes in Wide Peak

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

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

Genes
LRP1B

Genes in Wide Peak

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

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

Genes
FBXO25
C8orf42
ERICH1
ZNF596
LOC286083
OR4F21
RPL23AP53

Genes in Wide Peak

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

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

Genes
PTEN
KLLN

Genes in Wide Peak

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

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

Genes
FAM190A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q37.3.

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

Genes
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
AGXT
KIF1A
BOK
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PDCD1
PPP1R7
PER2
LRRFIP1
HDAC4
FARP2
RAMP1
STK25
COPS8
CAPN10
PASK
ATG4B
SNED1
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
HES6
CXCR7
RNPEPL1
GAL3ST2
RAB17
MLPH
IQCA1
C2orf54
ILKAP
ING5
MGC16025
AGAP1
TWIST2
NEU4
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
LOC151171
LOC151174
LOC200772
CXXC11
DUSP28
ESPNL
RBM44
AQP12A
KLHL30
OR6B2
ASB18
FLJ43879
MIR149
LOC643387
PRR21
AQP12B
D2HGDH
LOC728323
PP14571
BOK-AS1
MIR4269
UBE2F-SCLY
MIR2467
MIR4440
MIR4786
MIR4441

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q13.2.

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

Genes
PIK3R1
BTF3
CCNB1
CDK7
CRHBP
F2R
F2RL1
F2RL2
FOXD1
GTF2H2
HEXB
HMGCR
TNPO1
MAP1B
NAIP
PMCHL2
RAD17
SMN1
SMN2
TAF9
TBCA
SERF1A
ENC1
PDE8B
CARTPT
COL4A3BP
NSA2
IQGAP2
SMA4
SMA5
SV2C
MRPS27
OTP
FAM169A
GCNT4
POLK
AGGF1
WDR41
BDP1
ANKRA2
MCCC2
RGNEF
SLC30A5
CENPH
PTCD2
UTP15
ZBED3
GFM2
MRPS36
FCHO2
TMEM171
TMEM174
POC5
MARVELD2
ZNF366
S100Z
CCDC125
ANKRD31
LOC647859
GUSBP3
GTF2H2B
SNORA47
GTF2H2C
SERF1B
LOC728723
GTF2H2D
GUSBP9
LOC100170939
LOC100272216
NCRUPAR
OCLN
MIR4804
MIR4803

Genes in Wide Peak

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

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

Genes
CLEC3A
WWOX

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p21.2.

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

Genes
PPP2R2A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q34.13.

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

Genes
ABL1
NOTCH1
RALGDS
TSC1
BRD3
NUP214
FNBP1
hsa-mir-4292
hsa-mir-126
ABCA2
ABO
ASS1
C8G
ENTPD2
CEL
CELP
COL5A1
DBH
SARDH
TOR1A
FCN1
FCN2
FUT7
RAPGEF1
GRIN1
LCN1
PAEP
PTGDS
RPL7A
RXRA
SNAPC4
SURF1
SURF2
SURF4
MED22
SURF6
TRAF2
TTF1
VAV2
LHX3
GFI1B
SSNA1
EDF1
FUBP3
CLIC3
GTF3C5
GTF3C4
MED27
PTGES
ADAMTSL2
PPP1R26
SEC16A
LAMC3
TUBB4B
UBAC1
OLFM1
AGPAT2
POMT1
SDCCAG3
USP20
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
MAN1B1
SETX
PMPCA
EXOSC2
NCS1
COBRA1
GPSM1
DKFZP434A062
GBGT1
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
NDOR1
TOR1B
PHPT1
ANAPC2
DPP7
OBP2B
OBP2A
MRPS2
EGFL7
PRRX2
C9orf78
FBXW5
C9orf167
C9orf86
INPP5E
NPDC1
BARHL1
REXO4
KCNT1
GPR107
PRDM12
CARD9
DDX31
AIF1L
UCK1
NTNG2
PRRC2B
PPAPDC3
FIBCD1
KIAA1984
SNHG7
TMEM141
SAPCD2
C9orf69
UAP1L1
TMEM203
NACC2
C9orf116
LCN8
FAM69B
ASB6
SLC34A3
CAMSAP1
C9orf163
MAMDC4
LCN6
AK8
C9orf96
QSOX2
LINC00094
LCN12
C9orf142
TPRN
FAM78A
QRFP
GLT6D1
C9orf169
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
LCN9
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
MIR126
LCN10
C9orf173
NRARP
FAM163B
RNF224
SNORA17
SNORA43
SNORD62B
RNF208
DNLZ
LOC100128593
LOC100129722
LOC100130954
LOC100131193
RNU6ATAC
LOC100272217
LOC100289341
MIR4292
MIR3621
MIR3689A
MIR3689B
LOC100506599
MIR3689D1
MIR3689F
MIR4669
MIR4673
MIR4674
MIR3689C
MIR3689D2
MIR3689E
MIR4479

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q23.3.

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

Genes
GPHN
hsa-mir-625
hsa-mir-548h-1
ACTN1
ARG2
ZFP36L1
EIF2S1
ERH
ESR2
FNTB
FUT8
GPX2
HSPA2
MAX
MAP3K9
MTHFD1
PIGH
PPP2R5E
RAD51B
SRSF5
SLC8A3
SLC10A1
SPTB
ZBTB25
ADAM21
ADAM20
DCAF5
AKAP5
RGS6
KIAA0247
MED6
VTI1B
ZBTB1
PCNX
SYNE2
ZFYVE26
TTC9
PLEKHG3
SIPA1L1
PLEK2
KCNH5
RDH11
COX16
ATP6V1D
EXD2
SYNJ2BP
SLC39A9
C14orf162
RHOJ
GALNTL1
PLEKHH1
SMOC1
MPP5
SGPP1
SYT16
CHURC1
WDR89
GPHB5
RDH12
ADAM21P1
PPP1R36
LOC145474
FAM71D
TMEM229B
C14orf55
SNORD56B
RAB15
PLEKHD1
LINC00238
TEX21P
LOC645431
FLJ43390
LOC100289511
LOC100506321
SYNJ2BP-COX16
CHURC1-FNTB
MIR4708
MIR4706

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p26.3.

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

Genes
IL5RA
ITPR1
SETMAR
BHLHE40
EDEM1
CHL1
CNTN6
TRNT1
CRBN
ARL8B
LRRN1
CNTN4
SUMF1
EGOT
LOC100507582
MIR4790

Genes in Wide Peak

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

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

Genes
CREBBP

Genes in Wide Peak

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

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

Genes
GOLGA3
MMP17
POLE
PXMP2
SFSWAP
ZNF10
ZNF26
ZNF84
ZNF140
ULK1
ZNF268
P2RX2
ANKLE2
GALNT9
CHFR
EP400
FBRSL1
NOC4L
PUS1
PGAM5
DDX51
EP400NL
LOC647589
SNORA49
LOC100130238
ZNF605
LOC100507055

Genes in Wide Peak

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

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

Genes
A1BG
RPS5
ZNF8
MZF1
ZNF132
ZNF135
UBE2M
TRIM28
ZNF256
ZNF274
SLC27A5
ZNF324
CHMP2A
ZNF544
ZNF446
ZSCAN18
MGC2752
ZNF329
ZNF606
ZBTB45
ZNF837
C19orf18
ZNF418
ZNF417
ZNF497
ZNF584
ZSCAN1
ZSCAN22
ZNF324B
A1BG-AS1
LOC646862
ZNF814
LOC100128398
LOC100131691
MIR4754

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.3.

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

Genes
DUX4
hsa-mir-202
hsa-mir-378c
hsa-mir-4297
ADAM8
BNIP3
CYP2E1
ECHS1
INPP5A
MGMT
UTF1
GLRX3
DPYSL4
TUBGCP2
DUX2
VENTX
CALY
TTC40
PPP2R2D
LRRC27
GPR123
NKX6-2
KNDC1
MTG1
SYCE1
PRAP1
ZNF511
CTAGE7P
C10orf91
PWWP2B
PAOX
EBF3
TCERG1L
C10orf125
JAKMIP3
STK32C
LOC387723
FLJ46300
LOC399829
SPRNP1
FRG2B
SPRN
MIR202
LOC619207
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
MIR378C
MIR4297
MIR3944

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q23.1.

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

Genes
ANKS1B
FAM71C

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p21.1.

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

Genes
FHIT
BAP1
PBRM1
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
C3orf51
CACNA1D
SLC25A20
CISH
COL7A1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
FLNB
GNAI2
GNAT1
GPX1
GRM2
HYAL1
IMPDH2
ITIH1
ITIH3
ITIH4
LAMB2
MST1
MST1R
PDHB
PFKFB4
PLXNB1
PRKAR2A
PRKCD
QARS
RPL29
SEMA3F
NEK4
TCTA
TKT
TNNC1
UBA7
USP4
UQCRC1
WNT5A
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
ACOX2
HYAL3
HYAL2
HESX1
BSN
RRP9
CACNA2D2
VPRBP
IP6K1
PARP3
RBM6
RBM5
TRAIP
ARIH2
NPRL2
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
TUSC2
TWF2
LAMB2P1
RAD54L2
STAB1
FAM208A
NAT6
ABHD14A
POC1A
NDUFAF3
DNAH1
ERC2
APPL1
GNL3
SPCS1
RBM15B
GMPPB
ARHGEF3
C3orf18
SHISA5
ZMYND10
TEX264
CCDC72
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
P4HTM
IL17RD
QRICH1
PXK
DALRD3
CHDH
IL17RB
CACNA2D3
DCP1A
GLT8D1
SEMA3G
PCBP4
ABHD6
LRTM1
SELK
RNF123
CCDC71
NT5DC2
SLC26A6
CAMKV
CCDC51
WDR82
ATRIP
NICN1
MON1A
ABHD14B
UCN2
RFT1
ACTR8
GPR62
FAM3D
IQCF1
GLYCTK
PPM1M
C3orf45
ASB14
C3orf67
KCTD6
KLHDC8B
DNAH12
PDE12
FAM116A
FBXW12
CCDC66
CCDC36
SPATA12
C3orf62
TMEM110
AMIGO3
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
IQCF3
MIRLET7G
MIR135A1
MIR191
TMEM89
IQCF6
C3orf78
MIR425
C3orf71
LOC646498
SNORD19
SNORD69
ESRG
SNORD19B
C3orf74
BSN-AS2
MIR711
MIR4271
MIR3938
IQCF4
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
LUST

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q14.3.

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

Genes
hsa-mir-548p
hsa-mir-583
hsa-mir-2277
hsa-mir-9-2
hsa-mir-4280
ARSB
BHMT
CAST
CCNH
CETN3
CHD1
CKMT2
COX7C
CRHBP
HAPLN1
VCAN
DHFR
F2R
F2RL1
F2RL2
GLRX
HEXB
HMGCR
LNPEP
MEF2C
MSH3
PAM
PCSK1
RASA1
RASGRF2
RPS23
TBCA
NR2F1
THBS4
XRCC4
ST8SIA4
ENC1
AP3B1
PDE8B
RAB9BP1
HOMER1
SCAMP1
TTC37
ZFYVE16
EDIL3
COL4A3BP
LHFPL2
NSA2
POLR3G
IQGAP2
RHOBTB3
ELL2
SV2C
PPIP5K2
OTP
SSBP2
BHMT2
FAM169A
RNU5E-1
RNU5D-1
DMGDH
GCNT4
POLK
ERAP1
GIN1
AGGF1
WDR41
RIOK2
ARRDC3
ERAP2
RGNEF
MCTP1
NUDT12
ATG10
SPATA9
FAM172A
GPR98
ZCCHC9
ANKRD32
ZBED3
GFM2
SPZ1
C5orf30
ATP6AP1L
LYSMD3
SLCO6A1
JMY
POU5F2
POC5
ACOT12
TMEM167A
MBLAC2
TMEM161B
ARSK
FAM81B
PAPD4
LIX1
FAM151B
S100Z
C5orf27
CMYA5
ANKRD31
SERINC5
KIAA0825
GPR150
NBPF22P
RGMB
RFESD
ANKRD34B
FAM174A
MTX3
SLCO4C1
MIR9-2
CRSP8P
FLJ42709
FLJ35946
LOC644936
LINC00461
SCARNA18
SNORA47
MIR583
LOC728723
LOC100129716
LOC100131067
LOC100133050
LOC100289230
NCRUPAR
MIR2277
MIR4280
MTRNR2L2
MIR3607
MIR3660
LOC100505894
MIR3977

Genes in Wide Peak

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

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

Genes
FLI1
APLP2
ETS1
KCNJ1
KCNJ5
NFRKB
OPCML
ST14
BARX2
ARHGAP32
ADAMTS8
IGSF9B
NCAPD3
ACAD8
B3GAT1
ZBTB44
THYN1
NTM
PRDM10
TP53AIP1
JAM3
GLB1L2
VPS26B
GLB1L3
TMEM45B
ADAMTS15
C11orf45
SPATA19
LOC283174
LOC283177
SNX19
LINC00167
LOC100128239
LOC100507392
MIR4697

Genes in Wide Peak

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

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

Genes
hsa-let-7c
hsa-mir-3118-5
hsa-mir-3156-3
BAGE
HSPA13
TPTE
NRIP1
USP25
RBM11
C21orf15
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
ANKRD30BP2
LIPI
ABCC13
POTED
LOC388813
ANKRD20A11P
MIRLET7C
MIR99A
TEKT4P2
MIR3156-3
MIR3687
MIR3648

Genes in Wide Peak

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

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

Genes
GNA11
SH3GL1
STK11
TCF3
hsa-mir-7-3
hsa-mir-637
hsa-mir-4321
hsa-mir-1909
AES
AMH
ATP5D
CIRBP
CSNK1G2
DAPK3
EEF2
EFNA2
GAMT
GNA15
GNG7
MKNK2
GPX4
MATK
GADD45B
NFIC
OAZ1
MAP2K2
RPS15
SGTA
TBXA2R
THOP1
TLE2
SF3A2
S1PR4
AP3D1
APBA3
CHAF1A
EBI3
APC2
HMG20B
SEMA6B
UQCR11
SBNO2
ZFR2
PIP5K1C
TIMM13
DAZAP1
SNORD37
TJP3
ITGB1BP3
SLC39A3
ZBTB7A
FZR1
SIRT6
PIAS4
LSM7
MBD3
PCSK4
C19orf24
PLEKHJ1
FEM1A
STAP2
BTBD2
CCDC94
C19orf10
NCLN
SPPL2B
SHD
REXO1
ZNF77
C19orf29
CELF5
FSD1
TLE6
ZNF556
UBXN6
FAM108A1
DOHH
KLF16
DOT1L
CREB3L3
HDGFRP2
LMNB2
RAX2
MUM1
MPND
ATCAY
MIDN
DPP9
REEP6
IZUMO4
SCAMP4
ADAT3
ZNF554
MRPL54
LRG1
TMIGD2
TNFAIP8L1
ZNF57
JSRP1
MOB3A
MFSD12
GIPC3
PLK5
CIRBP-AS1
C19orf25
ATP8B3
DIRAS1
ZNF555
ANKRD24
C19orf26
CSNK1G2-AS1
C19orf77
MIR7-3HG
ADAMTSL5
TMPRSS9
NDUFS7
C19orf35
ONECUT3
MEX3D
C19orf29-AS1
MIR7-3
PLIN5
LINGO3
MIR637
PLIN4
C19orf71
LOC100131094
LOC100288123
MIR1909
MIR1227
MIR4321
MIR4746

Genes in Wide Peak

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

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

Genes
MYCN
hsa-mir-3125
hsa-mir-4262
hsa-mir-548s
hsa-mir-4261
ACP1
APOB
RHOB
DDX1
E2F6
HPCAL1
ID2
KCNF1
KCNS3
MATN3
ODC1
RPS7
RRM2
SDC1
SOX11
ADAM17
TPO
TSSC1
VSNL1
PXDN
KLF11
ASAP2
TAF1B
ITGB1BP1
ROCK2
GREB1
LAPTM4A
RNF144A
PDIA6
MYCNOS
YWHAQ
MYT1L
LPIN1
PUM2
NTSR2
SH3YL1
TRIB2
GRHL1
TRAPPC12
NBAS
CPSF3
SNTG2
ATAD2B
ADI1
ALLC
KIDINS220
WDR35
RDH14
C2orf43
HS1BP3
COLEC11
SMC6
NOL10
FAM49A
RSAD2
NT5C1B
KLHL29
CMPK2
MBOAT2
TMEM18
OSR1
TTC32
C2orf50
PQLC3
LOC150622
FAM84A
GDF7
CYS1
ATP6V1C2
RNASEH1
FAM150B
IAH1
FLJ33534
LOC339788
LINC00299
LOC339822
MSGN1
GEN1
C2orf48
LOC386597
LOC400940
LINC00487
FLJ12334
FAM110C
LOC645949
LOC727982
RAD51AP2
LOC730811
SNORA80B
MIR4261
MIR3125
MIR4262
LOC100505964
LOC100506054
LOC100506274
LOC100506474
NT5C1B-RDH14
MIR4757
MIR4429

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q32.3.

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

Genes
hsa-mir-3122
hsa-mir-4260
hsa-mir-205
hsa-mir-29b-2
ATF3
CD34
CENPF
CR1
CR1L
CR2
CD55
ESRRG
HSD11B1
IRF6
KCNH1
KCNK2
LAMB3
CD46
NEK2
PLXNA2
PPP2R5A
PROX1
PTPN14
TGFB2
TRAF5
USH2A
SLC30A1
LPGAT1
INTS7
NSL1
RPS6KC1
DIEXF
FLVCR1
NENF
G0S2
RRP15
KCTD3
DTL
GPATCH2
TMEM206
BATF3
HHAT
RCOR3
SERTAD4
SMYD2
CAMK1G
VASH2
TRAF3IP3
LINC00467
ANGEL2
LYPLAL1
SPATA17
TATDN3
C1orf74
LOC148696
C1orf227
FAM71A
SYT14
RD3
MIR205
MIR29B2
MIR29C
C1orf133
MIR205HG
FLVCR1-AS1
LOC643723
SNORA16B
LOC728463
MIR4260
MIR3122
PROX1-AS1
LINC00538

Genes in Wide Peak

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

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

Genes
PAX7
RPL22
SDHB
TNFRSF14
PRDM16
MDS2
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
TNFRSF8
CDA
CDK11B
CDC42
CLCN6
CLCNKA
CLCNKB
CNR2
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
MEGF6
EPHA2
ENO1
EPHA8
EPHB2
MTOR
FUCA1
GABRD
GALE
GNB1
ZBTB48
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
MFAP2
MTHFR
NBL1
NPPA
NPPB
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PRKCZ
RAP1GAP
RPL11
RSC1A1
SCNN1D
SKI
SLC2A5
SRM
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
LUZP1
PRDM2
MMP23B
MMP23A
KCNAB2
AKR7A2
ALDH4A1
EIF4G3
TNFRSF25
TNFRSF18
PER3
DHRS3
VAMP3
H6PD
ISG15
PLCH2
CROCC
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
CELA3A
ANGPTL7
HNRNPR
UBE4B
MAD2L2
PDPN
MASP2
SRSF10
UTS2
RER1
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
CLSTN1
AKR7A3
SPEN
KDM1A
KIAA0090
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
CHD5
C1orf144
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
HSPB7
ARHGEF16
LINC00339
SSU72
UBIAD1
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
SDF4
MRTO4
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
FBLIM1
PQLC2
CASZ1
CPSF3L
C1orf159
AURKAIP1
MRPL20
TMEM51
ARHGEF10L
VPS13D
ATAD3A
PANK4
CAMK2N1
ASAP3
PNRC2
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
CTNNBIP1
AGTRAP
PITHD1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
MIIP
CELA2A
PLA2G2F
NMNAT1
VWA1
PINK1
PRAMEF1
PRAMEF2
NADK
EFHD2
MMEL1
RSG1
OR4F5
MUL1
NOL9
AGMAT
LINC00115
MORN1
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
CCNL2
ESPN
TAS1R3
ATAD3B
PLEKHN1
USP48
NBPF3
SLC25A33
DDI2
LZIC
C1orf170
CROCCP2
IGSF21
KIAA1751
KIAA2013
THAP3
C1orf158
FBXO44
CROCCP3
FHAD1
LOC115110
RBP7
ACAP3
UBE2J2
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
C1orf64
SLC2A7
CALML6
FAM43B
TMEM201
C1orf86
C1orf126
ATAD3C
AKR7L
LOC254099
TTLL10
TMCO4
NPHP4
FAM41C
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
TMEM240
TMEM52
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
PRAMEF4
PRAMEF13
SH2D5
RNF223
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
ANKRD65
PRAMEF7
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC649330
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SNORA59B
SNORA59A
MIR551A
CDK11A
SLC35E2B
LOC728716
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
NPPA-AS1
MIR3115
MIR4253
MIR4251
MIR4252
MIR3675
ENO1-AS1
LOC100506730
LOC100506801
LOC100506963
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4684
MIR4689
MIR4632
MIR4417
MIR378F

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q22.3.

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

Genes
TMPRSS2
hsa-mir-3197
ADARB1
AIRE
PTTG1IP
C21orf2
CBS
COL6A1
COL6A2
CRYAA
CSTB
PRMT2
ITGB2
LSS
MX1
MX2
NDUFV3
PCNT
PDE9A
PFKL
PKNOX1
PWP2
S100B
SLC19A1
SUMO3
TFF1
TFF2
TFF3
TRAPPC10
TRPM2
U2AF1
UBE2G2
C21orf33
PDXK
RRP1
MCM3AP
ABCG1
WDR4
FTCD
HSF2BP
RRP1B
DIP2A
POFUT2
ICOSLG
BACE2
C2CD2
DNMT3L
ZNF295
UBASH3A
SLC37A1
PCBP3
C21orf58
YBEY
TSPEAR
LINC00112
LINC00111
FAM3B
RIPK4
AGPAT3
PRDM15
TMPRSS3
COL18A1
LRRC3
C21orf56
C21orf67
FAM207A
RSPH1
UMODL1
LINC00313
C21orf90
MCM3AP-AS1
SIK1
LINC00479
ZNF295-AS1
C21orf128
PLAC4
LINC00315
LINC00319
LOC284837
KRTAP12-2
KRTAP12-1
KRTAP10-10
LINC00162
COL18A1-AS1
KRTAP10-4
KRTAP10-6
KRTAP10-7
KRTAP10-9
KRTAP10-1
KRTAP10-11
KRTAP10-2
KRTAP10-5
KRTAP10-8
KRTAP10-3
KRTAP12-3
KRTAP12-4
KRTAP10-12
LOC642852
LINC00163
SSR4P1
LOC100129027
MIR3197
LOC100505746

Genes in Wide Peak

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

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

Genes
CDH1
CDH3
ZFP90

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p24.3.

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

Genes
JAK2
CD274
hsa-mir-101-2
hsa-mir-1302-9
DMRT1
FOXD4
MLANA
GLDC
INSL4
RFX3
RLN1
RLN2
SLC1A1
SMARCA2
VLDLR
KIAA0020
RCL1
DMRT2
INSL6
KDM4C
KANK1
RANBP6
AK3
C9orf68
CDC37L1
C9orf46
CBWD1
KIAA1432
DMRT3
ERMP1
PDCD1LG2
DOCK8
GLIS3-AS1
TPD52L3
IL33
UHRF2
C9orf66
KIAA2026
KCNV2
GLIS3
FLJ35024
PPAPDC2
MIR101-2
FAM138C
WASH1
MIR4665

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.3.

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

Genes
CBFA2T3
FANCA
AFG3L1P
APRT
C16orf3
CDH15
CYBA
DPEP1
GALNS
GAS8
MC1R
MVD
CHMP1A
RPL13
SPG7
CDK10
C16orf7
PIEZO1
TUBB3
PRDM7
TCF25
CPNE7
IL17C
ANKRD11
TRAPPC2L
DEF8
DBNDD1
CDT1
SPIRE2
CENPBD1
ZNF276
RNF166
SPATA2L
C16orf55
ZC3H18
SLC22A31
MGC23284
ZNF778
ACSF3
LINC00304
SNAI3
CTU2
PABPN1L
LOC400558
SNORD68
LOC100128881
LOC100130015
LOC100287036
MIR4722

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.32.

Table S74. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ERCC2
hsa-mir-220c
hsa-mir-3191
hsa-mir-320e
hsa-mir-769
hsa-mir-642
APOC1
APOC1P1
APOC2
APOC4
APOE
BCAT2
C5AR1
CA11
CALM3
CKM
AP2S1
CLPTM1
CRX
DBP
DMPK
DMWD
EMP3
ERCC1
FOSB
FUT1
FUT2
GIPR
GPR4
GRIN2D
ARHGAP35
FOXA3
KCNJ14
LIG1
NOVA2
NPAS1
PPP5C
PTGIR
RELB
RPL18
RTN2
SEPW1
SLC1A5
SLC8A2
SNRPD2
SULT2B1
SULT2A1
VASP
SYMPK
PLA2G4C
NAPA
PGLYRP1
CYTH2
DHX34
SAE1
TOMM40
PPP1R13L
CD3EAP
KDELR1
CLASRP
KPTN
CARD8
ZC3H4
FBXO46
SYNGR4
EML2
PRKD2
CCDC9
IRF2BP1
FGF21
BBC3
GPR77
STRN4
GLTSCR2
GLTSCR1
EHD2
QPCTL
FAM83E
RASIP1
TMEM160
PNMAL1
TMEM143
CABP5
SPHK2
MEIS3
PNMAL2
MARK4
ELSPBP1
HIF3A
TRAPPC6A
FKRP
GEMIN7
OPA3
RSPH6A
GRWD1
CCDC8
ZNF541
EXOC3L2
CCDC114
DKFZp434J0226
GNG8
LMTK3
NTN5
PPM1N
KLC3
DACT3
SIX5
IGFL2
ZNF296
ZNF114
SPACA4
PRR24
PPP1R37
NKPD1
TPRX1
MAMSTR
IZUMO1
MYPOP
NANOS2
IGFL1
BLOC1S3
LOC388553
IGFL3
MIR330
IGFL4
SEC1
SNORD23
MIR642A
CCDC61
MIR769
SNAR-A1
SNAR-A2
SNAR-A12
BSPH1
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-C1
SNAR-C3
SNAR-A14
LOC100287177
MIR3191
MIR3190
MIR320E
MIR642B
LOC100505681
LOC100505812
LOC100506012
LOC100506068
APOC4-APOC2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q11.

Table S75. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
FGF9
GJA3
GJB2
SGCG
TUBA3C
ZMYM2
IFT88
ZMYM5
SAP18
GJB6
SACS
LATS2
CRYL1
IL17D
MPHOSPH8
PSPC1
XPO4
MRP63
TPTE2
N6AMT2
SKA3
EFHA1
ZDHHC20
PHF2P1
ANKRD20A9P
LINC00442
BASP1P1
ANKRD26P3
LINC00421
MIR4499

Genes in Wide Peak

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

Table S76. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
IRF4
FOXF2
FOXC1
GMDS
EXOC2
DUSP22
FOXQ1
HUS1B
LOC285768
LOC100508120

Genes in Wide Peak

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

Table S77. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
JAK1
NRAS
BCL10
TRIM33
RBM15
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
hsa-mir-186
hsa-mir-1262
hsa-mir-3117
hsa-mir-101-1
ABCA4
ACADM
ADORA3
AGL
AK4
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CRYZ
CSF1
CTBS
CTH
DBT
GADD45A
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
GBP1
GBP2
GBP3
GFI1
GCLM
GNAI3
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
IGSF3
CYR61
IL12RB2
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
LEPR
MOV10
MSH4
NGF
NHLH2
ROR1
OVGP1
PDE4B
PGM1
PIN1P1
PRKACB
PKN2
PSMA5
PTGER3
PTGFR
PTGFRN
ABCD3
RABGGTB
RAP1A
SNORD21
RPE65
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TGFBR3
TSHB
VCAM1
WNT2B
CSDE1
EVI5
CDC7
BCAR3
TTF2
LMO4
CDC14A
RTCD1
FPGT
FUBP1
DIRAS3
SLC16A4
SRSF11
CD101
SEP15
ZRANB2
ARHGAP29
CLCA3P
CLCA2
HS2ST1
DNAJC6
LRIG2
LPPR4
INSL5
PIGK
TSPAN2
BCAS2
CEPT1
VAV3
HBXIP
IFI44
AP4B1
PHTF1
AHCYL1
MAN1A2
IFI44L
DNAJB4
GLMN
HHLA3
DDX20
CLCA4
MTF2
NTNG1
WDR47
USP33
CLCC1
SLC35D1
LPHN2
KIAA1107
ITGB3BP
SLC35A3
LRRC8B
LPAR3
DDAH1
RWDD3
ZZZ3
SERBP1
PTPN22
AK5
SNORA66
SNORD45B
SNORD45A
FOXD3
CHIA
GPSM2
ALG6
SLC25A24
DNTTIP2
TMED5
TNNI3K
SH3GLB1
SNX7
DPH5
GPR88
CCDC76
RSBN1
ZNHIT6
LEPROT
GIPC2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
RAVER2
MCOLN3
SLC22A15
RNPC3
LRRC40
DEPDC1
LRIF1
CTTNBP2NL
FAM212B
GNG12
CCBL2
TMEM167B
OLFML3
AMIGO1
ODF2L
KIAA1324
LRRC7
CACHD1
MIER1
PTBP2
DNASE2B
ELTD1
HIAT1
DCLRE1B
WDR77
DLEU2L
EPS8L3
VTCN1
TTLL7
WDR78
RPAP2
DENND2D
WLS
RPF1
SIKE1
TRIM45
ANKRD13C
VANGL1
ST6GALNAC5
GPR61
SYDE2
ZNF644
LRRC8C
SGIP1
PROK1
EFCAB7
PSRC1
ATP1A1OS
FAM40A
NEXN
DNAJA1P5
HENMT1
GBP4
GBP5
SSX2IP
OLFM3
WDR63
MAB21L3
SLC44A3
ATXN7L2
C1orf194
ASB17
TYW3
C1orf173
LRRIQ3
LRRC39
DRAM2
C1orf88
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
UBE2U
SLC30A7
MGC27382
IL23R
RP11-165H20.1
DENND2C
GBP6
LPPR5
FNDC7
SASS6
HFM1
UBL4B
ALG14
TCTEX1D1
HIPK1
SLC44A5
AKR7A2P1
EPHX4
AKNAD1
MCOLN2
COL24A1
ST6GALNAC3
NEGR1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
ZNF326
BTBD8
PPM1J
LOC339524
CCDC18
MYBPHL
BARHL2
HSP90B3P
FAM73A
GBP7
C1orf146
FAM69A
SLC6A17
UOX
FRRS1
C1orf141
GBP1P1
FLJ27354
MIR137HG
MIR101-1
MIR137
MIR186
MIR197
LHX8
C1orf180
FLJ31662
LOC440600
BCL2L15
PGCP1
GEMIN8P4
RBMXL1
SRG7
CYMP
LOC643441
LOC646626
LOC648740
NBPF6
SCARNA2
SNORD45C
MIR548D1
MIR553
LOC729970
LOC729987
MIR942
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129269
LOC100129620
LOC100131564
ZRANB2-AS1
LOC100287722
LOC100289178
MIR320B1
MIR1262
MIR3117
MIR4256
MIR3671
MIR548AA1
LOC100505768
LOC100506343
FPGT-TNNI3K
TMEM56-RWDD3
MIR4794
MIR2682
MIR4423
NEGR1-IT1
ZRANB2-AS2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p15.3.

Table S78. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ADARB2
KLF6
IDI1
PFKP
PITRM1
ZMYND11
WDR37
DIP2C
LARP4B
GTPBP4
IDI2-AS1
IDI2
LOC282980
TUBB8
LINC00200
LOC399708
C10orf108
ADARB2-AS1
LOC100507034

Genes in Wide Peak

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

Table S79. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
MAP2K4
hsa-mir-744
MIR744

Genes in Wide Peak

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

Table S80. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
LSAMP-AS3

Arm-level results

Table 3. Get Full Table Arm-level significance table - 29 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.21 | 0.131 | 1 | 0.10 | -5.72 | 1
1q | 1955 | 0.34 | 6.49 | 4.26e-10 | 0.09 | -6.29 | 1
2p | 924 | 0.27 | -2.25 | 1 | 0.07 | -10.7 | 1
2q | 1556 | 0.22 | -2.32 | 1 | 0.07 | -9.07 | 1
3p | 1062 | 0.23 | -3.6 | 1 | 0.20 | -4.8 | 1
3q | 1139 | 0.49 | 9.71 | 0 | 0.13 | -6.32 | 1
4p | 489 | 0.14 | -7.22 | 1 | 0.57 | 9.97 | 0
4q | 1049 | 0.07 | -7.69 | 1 | 0.60 | 15 | 0
5p | 270 | 0.38 | -0.0033 | 1 | 0.39 | 0.442 | 0.558
5q | 1427 | 0.11 | -6.68 | 1 | 0.43 | 7.95 | 2.44e-15
6p | 1173 | 0.40 | 4.54 | 2.21e-05 | 0.41 | 5.18 | 2.27e-07
6q | 839 | 0.21 | -4.45 | 1 | 0.51 | 8.78 | 0
7p | 641 | 0.31 | -1.64 | 1 | 0.28 | -2.82 | 1
7q | 1277 | 0.36 | 3.46 | 0.0013 | 0.17 | -5.03 | 1
8p | 580 | 0.28 | -2.08 | 1 | 0.69 | 16.1 | 0
8q | 859 | 0.53 | 9.57 | 0 | 0.32 | -0.0999 | 0.877
9p | 422 | 0.23 | -4.59 | 1 | 0.55 | 8.66 | 0
9q | 1113 | 0.10 | -7.39 | 1 | 0.53 | 11.4 | 0
10p | 409 | 0.33 | -1.49 | 1 | 0.26 | -4.24 | 1
10q | 1268 | 0.16 | -5.66 | 1 | 0.27 | -1.02 | 1
11p | 862 | 0.13 | -7.95 | 1 | 0.38 | 2.69 | 0.0067
11q | 1515 | 0.21 | -2.54 | 1 | 0.29 | 1.12 | 0.231
12p | 575 | 0.44 | 4.25 | 6.98e-05 | 0.23 | -4.74 | 1
12q | 1447 | 0.27 | -0.212 | 1 | 0.25 | -1.15 | 1
13q | 654 | 0.19 | -5.48 | 1 | 0.55 | 9.64 | 0
14q | 1341 | 0.09 | -7.87 | 1 | 0.39 | 5.4 | 7.06e-08
15q | 1355 | 0.08 | -8.11 | 1 | 0.44 | 8.21 | 2.89e-16
16p | 872 | 0.13 | -6.48 | 1 | 0.58 | 12.5 | 0
16q | 702 | 0.10 | -6.39 | 1 | 0.73 | 19.1 | 0
17p | 683 | 0.14 | -4.77 | 1 | 0.80 | 22.7 | 0
17q | 1592 | 0.17 | -2.87 | 1 | 0.64 | 20.1 | 0
18p | 143 | 0.25 | -5.3 | 1 | 0.46 | 3.11 | 0.00183
18q | 446 | 0.15 | -7.34 | 1 | 0.55 | 8.79 | 0
19p | 995 | 0.29 | -0.992 | 1 | 0.46 | 6.77 | 1.5e-11
19q | 1709 | 0.24 | -0.227 | 1 | 0.44 | 9.59 | 0
20p | 355 | 0.46 | 4.13 | 0.000102 | 0.16 | -7.87 | 1
20q | 753 | 0.51 | 8.75 | 0 | 0.10 | -8.46 | 1
21q | 509 | 0.19 | -6.71 | 1 | 0.34 | -0.878 | 1
22q | 921 | 0.08 | -6.58 | 1 | 0.73 | 20.7 | 0

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.

- 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.

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/OV/1551689/2.GDAC_MergeDataFiles.Finished/OV.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 = 0.30

- Deletion Threshold = 0.30

- Cap Values = 2.0

- Broad Length Cutoff = 0.5

- Remove X-Chromosome = 1

- Confidence Level = 0.99

- Join Segment Size = 10

- Arm Level Peel Off = 1

- Maximum Sample Segments = 10000

Table 4. Get Full Table First 10 out of 558 Input Tumor Samples.

Tumor Sample Names
TCGA-04-1331-01A-01D-0428-01
TCGA-04-1332-01A-01D-0428-01
TCGA-04-1335-01A-01D-0428-01
TCGA-04-1336-01A-01D-0428-01
TCGA-04-1337-01A-01D-0428-01
TCGA-04-1338-01A-01D-0428-01
TCGA-04-1341-01A-01D-0428-01
TCGA-04-1342-01A-01D-0428-01
TCGA-04-1343-01A-01D-0428-01
TCGA-04-1346-01A-01D-0428-01

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:

1. Unique Name: A name assigned to identify the region.

2. Descriptor: The genomic descriptor of that region.

3. 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.

4. Peak Limits: The boundaries of the region of maximal amplification or deletion.

5. Region Limits: The boundaries of the entire significant region of amplification or deletion.

6. Q values: The Q value of the peak region.

7. 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.

8. 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').

9. 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:

1. Cytoband

2. Q value

3. Residual Q value

4. 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

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

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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