Uterine Corpus Endometrioid Carcinoma: 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 428 tumor samples used in this analysis: 23 significant arm-level results, 43 significant focal amplifications, and 45 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 - 43 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
17q12 | 4.0672e-23 | 2.1434e-19 | chr17:37827871-37877201 | 2
19q12 | 1.8918e-18 | 1.8918e-18 | chr19:30306821-30358071 | 1
8q24.21 | 2.943e-25 | 1.6826e-13 | chr8:129532671-129557624 | 0 [MIR1208]
8q24.21 | 1.1479e-24 | 5.7542e-12 | chr8:128739772-128781734 | 1
3q26.2 | 1.2236e-19 | 1.8422e-10 | chr3:168677469-168740350 | 0 [MECOM]
3p25.1 | 1.3405e-08 | 1.3405e-08 | chr3:13714839-13726839 | 1
10q22.2 | 6.6052e-08 | 6.6052e-08 | chr10:76700603-77071885 | 7
1p22.3 | 1.0128e-07 | 3.2762e-07 | chr1:85974031-86006008 | 1
20q11.21 | 2.1467e-08 | 6.1722e-07 | chr20:30731473-30798667 | 4
1q21.3 | 4.5919e-10 | 1.6604e-06 | chr1:151198872-151321504 | 5
3q26.2 | 1.0109e-13 | 3.0074e-06 | chr3:169358143-169507091 | 4
2q13 | 3.5866e-06 | 3.5866e-06 | chr2:113953684-114236549 | 4
1q22 | 1.2791e-09 | 3.9092e-06 | chr1:155922230-156101508 | 7
6p24.2 | 7.6977e-06 | 7.6977e-06 | chr6:11230043-11530964 | 1
8p11.21 | 3.3436e-06 | 9.231e-06 | chr8:41558899-42054928 | 4
12q13.2 | 2.5021e-06 | 3.1254e-05 | chr12:56481350-56491606 | 1
11q13.2 | 0.00030002 | 0.00041514 | chr11:67294199-67775127 | 9
5p15.33 | 0.0004664 | 0.0004664 | chr5:1-1325802 | 25
4p16.3 | 0.00075689 | 0.00075689 | chr4:1512439-1881446 | 7
19p13.2 | 8.7863e-06 | 0.00092259 | chr19:10856140-10927539 | 2
16p11.2 | 0.0010401 | 0.0010401 | chr16:30854953-31009587 | 11
17q11.2 | 5.3144e-05 | 0.0011086 | chr17:27064353-27113673 | 3
9p24.2 | 0.0050634 | 0.0050634 | chr9:3631009-3996780 | 2
18q11.2 | 0.0058464 | 0.0058464 | chr18:23786856-24107630 | 2
17q21.32 | 0.00045215 | 0.0085802 | chr17:46458792-46639145 | 4
19p13.13 | 0.00016888 | 0.015128 | chr19:13803150-14008602 | 13
1p34.2 | 0.010171 | 0.020113 | chr1:41336196-41507861 | 4
20q13.12 | 0.0048214 | 0.032884 | chr20:45875493-46137215 | 3
14q24.3 | 0.019126 | 0.052233 | chr14:77305985-77410930 | 1
9q34.3 | 0.078531 | 0.078531 | chr9:139793924-139897193 | 8
7q22.1 | 0.083416 | 0.083416 | chr7:99523615-99827234 | 24
2p23.2 | 0.098282 | 0.098282 | chr2:1-29263496 | 195
20q13.33 | 0.010171 | 0.12193 | chr20:62032672-63025520 | 43
11p11.2 | 0.12712 | 0.12712 | chr11:46300642-46481485 | 9
12q13.11 | 0.0026397 | 0.13039 | chr12:48093285-48305012 | 6
12p13.33 | 0.14279 | 0.14279 | chr12:1-3229930 | 34
6q16.3 | 0.16143 | 0.16143 | chr6:104856105-108506044 | 21
8p11.22 | 0.024197 | 0.19592 | chr8:33893071-39206994 | 30
14q32.32 | 0.078531 | 0.19592 | chr14:103918030-104368348 | 10
11q22.2 | 0.19211 | 0.22245 | chr11:102273095-102512085 | 3
15q26.3 | 0.23923 | 0.23923 | chr15:98000287-102531392 | 35
17p11.2 | 0.17204 | 0.24991 | chr17:20068572-20517009 | 5
20p13 | 0.24991 | 0.24991 | chr20:1-4914871 | 97

Genes in Wide Peak

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

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

Genes
ERBB2
PGAP3

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 8q24.21.

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

Genes
MYC

Genes in Wide Peak

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

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

Genes
LOC285375

Genes in Wide Peak

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

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

Genes
VDAC2
KAT6B
DUSP13
COMTD1
SAMD8
ZNF503-AS1
DUPD1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p22.3.

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

Genes
DDAH1

Genes in Wide Peak

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

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

Genes
PLAGL2
TM9SF4
POFUT1
TSPY26P

Genes in Wide Peak

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

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

Genes
PI4KB
PSMD4
RFX5
PIP5K1A
ZNF687

Genes in Wide Peak

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

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

Genes
MECOM
TERC
MYNN
ARPM1

Genes in Wide Peak

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

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

Genes
PAX8
PSD4
CBWD2
LOC654433

Genes in Wide Peak

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

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

Genes
LMNA
SSR2
ARHGEF2
LAMTOR2
UBQLN4
RAB25
MEX3A

Genes in Wide Peak

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

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

Genes
NEDD9

Genes in Wide Peak

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

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

Genes
ANK1
PLAT
KAT6A
AP3M2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q13.2.

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

Genes
ERBB3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.2.

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

Genes
ALDH3B2
GSTP1
NDUFV1
UNC93B1
ACY3
NUDT8
TBX10
DOC2GP
FAM86C2P

Genes in Wide Peak

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

Table S16. 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 4p16.3.

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

Genes
FGFR3
WHSC1
LETM1
SLBP
TACC3
TMEM129
FAM53A

Genes in Wide Peak

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

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

Genes
DNM2
MIR4748

Genes in Wide Peak

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

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

Genes
hsa-mir-762
CTF1
BCL7C
SETD1A
FBXL19
HSD3B7
ORAI3
STX1B
FBXL19-AS1
MIR762
MIR4519

Genes in Wide Peak

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

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

Genes
TRAF4
C17orf63
NEK8

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p24.2.

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

Genes
GLIS3-AS1
GLIS3

Genes in Wide Peak

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

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

Genes
TAF4B
KCTD1

Genes in Wide Peak

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

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

Genes
HOXB1
HOXB2
HOXB3
SKAP1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19p13.13.

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

Genes
hsa-mir-181d
C19orf53
ZSWIM4
C19orf57
CCDC130
MRI1
LOC284454
NANOS3
MIR181C
MIR23A
MIR24-2
MIR27A
MIR181D

Genes in Wide Peak

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

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

Genes
CTPS
SCMH1
SLFNL1
LOC100507178

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.12.

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

Genes
NCOA3
ZMYND8
LOC100131496

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q24.3.

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

Genes
C14orf166B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9q34.3.

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

Genes
C8G
PTGDS
TRAF2
CLIC3
FBXW5
LCN12
C9orf142
LCNL1

Genes in Wide Peak

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

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

Genes
hsa-mir-106b
AZGP1
MCM7
TAF6
ZNF3
ZKSCAN1
ZSCAN21
AP4M1
STAG3
COPS6
C7orf43
PVRIG
GAL3ST4
GPC2
CNPY4
MBLAC1
GJC3
GATS
C7orf59
MIR106B
MIR25
MIR93
AZGP1P1
MIR4658

Genes in Wide Peak

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

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

Genes
DNMT3A
MYCN
NCOA1
hsa-mir-4263
hsa-mir-1301
hsa-mir-3125
hsa-mir-4262
hsa-mir-548s
hsa-mir-4261
ACP1
ADCY3
APOB
RHOB
CAD
CENPA
DDX1
DTNB
E2F6
FKBP1B
FOSL2
FTH1P3
GCKR
GTF3C2
HADHA
HADHB
HPCAL1
ID2
KCNF1
KCNK3
KCNS3
KHK
KIF3C
MATN3
MPV17
ODC1
POMC
PPM1G
PPP1CB
RPS7
RRM2
SDC1
SOX11
ADAM17
TPO
TSSC1
UCN
VSNL1
SLC30A3
PXDN
KLF11
ASAP2
SLC5A6
EIF2B4
TAF1B
ITGB1BP1
OTOF
ROCK2
TP53I3
MRPL33
BRE
GREB1
LAPTM4A
RNF144A
SNX17
SUPT7L
PREB
PDIA6
MYCNOS
CGREF1
RAB10
YWHAQ
EMILIN1
GPN1
MAPRE3
SLC4A1AP
EFR3B
MYT1L
WDR43
LPIN1
PUM2
NTSR2
IFT172
SH3YL1
SNORD53
TRIB2
GRHL1
NRBP1
ITSN2
TRAPPC12
DNAJC27
C2orf28
NBAS
SF3B14
CPSF3
SNTG2
ATAD2B
TMEM214
C2orf18
TRMT61B
ASXL2
ADI1
ALLC
DPYSL5
TRIM54
KIDINS220
WDR35
RDH14
AGBL5
C2orf43
RBKS
HS1BP3
FNDC4
COLEC11
CENPO
CCDC121
SMC6
NOL10
C2orf44
FAM49A
C2orf16
ZNF512
ABHD1
EPT1
RSAD2
CCDC164
NT5C1B
KLHL29
CMPK2
MBOAT2
TMEM18
CIB4
OSR1
TTC32
ZNF513
C2orf50
PQLC3
LOC150622
TCF23
FAM59B
PLB1
FAM84A
GDF7
GPR113
FAM179A
UBXN2A
CYS1
KRTCAP3
SPDYA
ATP6V1C2
RNASEH1
FAM150B
DNAJC5G
IAH1
FLJ33534
C2orf70
C2orf53
LOC339788
LINC00299
LOC339822
MSGN1
GEN1
C2orf48
PFN4
LOC375190
LOC386597
MFSD2B
PTRHD1
LOC400940
LINC00487
FLJ12334
FAM110C
LOC645949
C2orf84
SNORD92
LOC727982
RAD51AP2
DNAJC27-AS1
LOC730811
OST4
MIR1301
LOC100302650
SNORA80B
MIR4261
MIR4263
MIR3125
MIR4262
LOC100505624
LOC100505716
LOC100505964
LOC100506054
LOC100506274
LOC100506474
NT5C1B-RDH14
MIR4757
MIR4429

Genes in Wide Peak

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

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

Genes
hsa-mir-647
EEF1A2
NPBWR2
KCNQ2
MYT1
OPRL1
PTK6
SRMS
TCEA2
TPD52L2
TNFRSF6B
ARFRP1
RGS19
PRPF6
GMEB2
STMN3
RTEL1
SOX18
LIME1
UCKL1
PCMTD2
SLC2A4RG
ZNF512B
C20orf195
PPDPF
DNAJC5
ZGPAT
PRIC285
ZBTB46
SAMD10
ABHD16B
LINC00266-1
C20orf201
LINC00176
MIR647
UCKL1-AS1
MIR941-1
MIR941-4
MIR941-2
MIR941-3
MIR1914
LOC100505815
RTEL1-TNFRSF6B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p11.2.

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

Genes
CREB3L1
hsa-mir-3160-2
CHRM4
MDK
DGKZ
AMBRA1
MIR3160-2
MIR3160-1
MIR4688

Genes in Wide Peak

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

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

Genes
VDR
ENDOU
RAPGEF3
HDAC7
SLC48A1
RPAP3

Genes in Wide Peak

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

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

Genes
KDM5A
CACNA1C
FKBP4
FOXM1
NINJ2
RAD52
SLC6A12
SLC6A13
TEAD4
TULP3
TSPAN9
ERC1
ITFG2
WNK1
ADIPOR2
WNT5B
C12orf32
NRIP2
CCDC77
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 6q16.3.

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

Genes
PRDM1
hsa-mir-587
AIM1
PREP
NR2E1
ATG5
BVES
SEC63
OSTM1
C6orf203
SOBP
QRSL1
PDSS2
HACE1
BEND3
POPDC3
RTN4IP1
BVES-AS1
SCML4
LIN28B
LOC100422737

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.22.

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

Genes
FGFR1
WHSC1L1
ADRB3
EIF4EBP1
STAR
TACC1
ADAM9
ASH2L
BAG4
ERLIN2
PROSC
DDHD2
GPR124
LSM1
BRF2
PLEKHA2
ZNF703
RAB11FIP1
TM2D2
PPAPDC1B
GOT1L1
UNC5D
LETM2
KCNU1
HTRA4
ADAM32
ADAM5P
RNF5P1
C8orf86
LOC728024

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q32.32.

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

Genes
CKB
KLC1
MARK3
XRCC3
BAG5
PPP1R13B
ZFYVE21
APOPT1
TRMT61A
LOC145216

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q22.2.

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

Genes
MMP7
MMP20
TMEM123

Genes in Wide Peak

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

Table S39. 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 17p11.2.

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

Genes
SPECC1
CDRT15L2
LGALS9B
CCDC144C
KRT16P3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20p13.

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

Genes
hsa-mir-103-2-as
hsa-mir-1292
ADRA1D
AVP
CDC25B
CENPB
CSNK2A1
FKBP1A
GNRH2
IDH3B
ITPA
OXT
PDYN
PRNP
PTPRA
SIGLEC1
SNRPB
SOX12
TCF15
TGM3
ATRN
PSMF1
SNPH
ProSAPiP1
RASSF2
SLC23A2
SIRPB1
NOP56
RBCK1
RNF24
UBOX5
PRND
SPEF1
C20orf194
SNORD57
SNORD56
SDCBP2
ANGPT4
SMOX
C20orf27
C20orf29
TMEM74B
SIRPG
NSFL1C
CPXM1
MAVS
EBF4
TRIB3
FASTKD5
GFRA4
VPS16
FAM113A
MRPS26
DDRGK1
ZNF343
NRSN2
PANK2
ADAM33
DEFB126
FAM110A
SLC4A11
ZCCHC3
SCRT2
C20orf54
HSPA12B
TMC2
TBC1D20
SIRPD
C20orf141
C20orf96
SRXN1
DEFB127
DEFB129
SIRPA
STK35
PRNT
DEFB125
DEFB128
SIRPB2
RSPO4
TGM6
DEFB132
C20orf202
MIR103A2
RAD21L1
SNORA51
SNORD86
SNORD110
LOC728228
SNORD119
LOC100134015
TMEM239
LOC100289473
MIR1292
MIR103B2
LOC100507495
FKBP1A-SDCBP2

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

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
19p13.3 | 1.2445e-32 | 1.2445e-32 | chr19:2299390-4675277 | 73
5q11.2 | 1.2134e-17 | 1.2134e-17 | chr5:58260298-59787985 | 3
2q22.1 | 4.5802e-16 | 1.5559e-15 | chr2:139655617-143637838 | 1
10q23.31 | 6.0464e-13 | 7.4516e-13 | chr10:89617158-90034038 | 2
4q34.3 | 3.3622e-16 | 1.0774e-11 | chr4:178911874-183060693 | 1
1p36.11 | 5.7074e-17 | 1.4529e-11 | chr1:26900639-27322419 | 9
6q26 | 5.7229e-11 | 5.657e-11 | chr6:161693099-163153207 | 1
16q23.1 | 1.7719e-10 | 3.6476e-09 | chr16:78129058-79627770 | 1
17q11.2 | 1.5093e-09 | 5.2717e-09 | chr17:29326736-29722618 | 5
11p15.5 | 4.6239e-07 | 4.6239e-07 | chr11:1-63334217 | 752
20p12.1 | 1.2793e-05 | 1.3192e-05 | chr20:14302876-16252980 | 3
22q13.32 | 9.0215e-06 | 1.9417e-05 | chr22:45095899-51304566 | 86
7p22.3 | 5.2058e-05 | 5.2058e-05 | chr7:1-2556638 | 34
12q23.1 | 2.726e-05 | 0.00014013 | chr12:99124001-100107912 | 2
3p14.2 | 0.00018031 | 0.00017264 | chr3:56500752-89453056 | 101
1p36.31 | 1.0774e-11 | 0.0003968 | chr1:1-23755512 | 365
8p23.3 | 1.4266e-05 | 0.00052995 | chr8:1-6262191 | 15
11q24.2 | 0.00012691 | 0.00058279 | chr11:118951924-135006516 | 145
18q23 | 0.00083507 | 0.00087969 | chr18:62012003-78077248 | 46
4q22.1 | 8.4742e-05 | 0.00095142 | chr4:90844993-93240505 | 1
22q12.1 | 0.00067393 | 0.0017781 | chr22:29192671-29455701 | 1
15q15.1 | 0.00020872 | 0.0018718 | chr15:31451831-47478056 | 180
7q36.1 | 0.00068683 | 0.0029407 | chr7:140393129-159138663 | 182
4p16.3 | 0.0048499 | 0.0047682 | chr4:1-1511830 | 31
17p13.3 | 0.0058998 | 0.007419 | chr17:1-1667971 | 34
12q24.33 | 0.0015221 | 0.0098312 | chr12:112941988-133851895 | 194
8p11.22 | 0.0010472 | 0.012357 | chr8:32399291-40388317 | 43
7q11.22 | 0.0026933 | 0.020254 | chr7:66780207-70601215 | 1
9p24.1 | 0.02247 | 0.0214 | chr9:7799607-12693402 | 1
13q14.2 | 0.0057445 | 0.0214 | chr13:48833767-49281290 | 3
11q14.1 | 0.0089118 | 0.0304 | chr11:82995735-85348794 | 2
16p13.3 | 0.036303 | 0.035898 | chr16:3455080-4013466 | 9
14q13.1 | 0.037929 | 0.038278 | chr14:1-39220018 | 212
2q37.3 | 0.0047682 | 0.043228 | chr2:209359189-243199373 | 297
10q21.2 | 0.031765 | 0.043228 | chr10:61512058-61718254 | 1
20q13.12 | 0.062583 | 0.059792 | chr20:45363767-45797806 | 1
9q34.11 | 0.075119 | 0.077649 | chr9:118156521-141213431 | 364
15q23 | 0.0070879 | 0.091748 | chr15:71180483-101718699 | 290
17p11.2 | 0.028402 | 0.091748 | chr17:17704545-17878202 | 4
13q11 | 0.031765 | 0.10821 | chr13:1-47346440 | 184
19q13.43 | 0.1136 | 0.10821 | chr19:38210512-59128983 | 829
16q22.2 | 0.00011542 | 0.15641 | chr16:31772318-90354753 | 440
17q21.2 | 0.0092245 | 0.17753 | chr17:31957152-46607558 | 371
22q11.1 | 0.01907 | 0.17753 | chr22:1-22114035 | 116
17p11.2 | 0.059254 | 0.18182 | chr17:19651612-20253412 | 3

Genes in Wide Peak

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

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

Genes
GNA11
SH3GL1
hsa-mir-637
AES
DAPK3
EEF2
GNA15
GNG7
MATK
GADD45B
NFIC
MAP2K2
SGTA
TBXA2R
THOP1
TLE2
S1PR4
APBA3
CHAF1A
EBI3
HMG20B
SEMA6B
ZFR2
PIP5K1C
TIMM13
SNORD37
TJP3
ITGB1BP3
SLC39A3
ZBTB7A
FZR1
SIRT6
PIAS4
LSM7
STAP2
CCDC94
C19orf10
NCLN
SPPL2B
SHD
ZNF77
C19orf29
CELF5
FSD1
TLE6
ZNF556
UBXN6
DOHH
CREB3L3
HDGFRP2
LMNB2
RAX2
MPND
ATCAY
ZNF554
MRPL54
LRG1
TMIGD2
TNFAIP8L1
ZNF57
MFSD12
GIPC3
DIRAS1
ZNF555
ANKRD24
C19orf77
TMPRSS9
C19orf29-AS1
PLIN5
MIR637
PLIN4
C19orf71
MIR4746

Genes in Wide Peak

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

Table S43. 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 2q22.1.

Table S44. 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 10q23.31.

Table S45. 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 4q34.3.

Table S46. 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 1p36.11.

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

Genes
ARID1A
SFN
NR0B2
NUDC
GPN2
PIGV
GPATCH3
ZDHHC18
C1orf172

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's Cancer Gene Census [7].

Genes
PARK2

Genes in Wide Peak

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

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

Genes
WWOX

Genes in Wide Peak

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

Table S50. 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 11p15.5.

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

Genes
CARS
DDB2
EXT2
FANCF
HRAS
LMO1
LMO2
NUP98
WT1
CREB3L1
hsa-mir-1908
hsa-mir-3162
hsa-mir-130a
hsa-mir-3161
hsa-mir-3160-2
hsa-mir-129-2
hsa-mir-610
hsa-mir-3159
hsa-mir-4299
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
ACP2
ADM
AP2A2
APLNR
AMPD3
APBB1
RHOG
ARHGAP1
ARNTL
ART1
ASCL2
BDNF
SERPING1
MPPED2
C11orf9
C11orf10
DAGLA
CALCA
CALCB
CAT
CCKBR
CD5
CD6
MS4A1
MS4A3
CD44
CD59
CD81
CD151
CDKN1C
CHRM1
CHRM4
TPP1
CNGA4
CNTF
COPB1
CRY2
CSTF3
CTNND1
CTSD
DDB1
DRD4
DUSP8
EEF1G
EIF4G2
ELF5
F2
MS4A2
FEN1
FOLH1
FSHB
FTH1
GAS2
GIF
GNG3
GTF2H1
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INCENP
INS
IRF7
CD82
KCNA4
KCNC1
KCNJ11
KCNQ1
LDHA
LDHC
FADS1
FADS3
LRP4
LSP1
CAPRIN1
MDK
SCGB2A1
SCGB2A2
MUC2
MUC6
MYBPC3
MYOD1
NAP1L4
NDUFS3
NELL1
NUCB2
SLC22A18
SLC22A18AS
OSBP
P2RX3
PAX6
PDE3B
PGA5
PIK3C2A
POLR2G
POLR2L
PRG2
PSMA1
PSMC3
PSMD13
PTH
PTPRJ
RAB3IL1
RAG1
RAG2
RAPSN
RARRES3
RCN1
RNH1
ROM1
MRPL23
RPL27A
RPLP2
RPS13
RRM1
SAA1
SAA2
SAA3P
SAA4
SCT
SLC1A2
SLC3A2
SMPD1
SPI1
TRIM21
SSRP1
ST5
STIM1
STX3
STX5
ABCC8
TAF10
TALDO1
TCN1
TEAD1
TH
TSPAN4
TNNI2
TNNT3
TPH1
TRAF6
TRPC2
TSG101
PHLDA2
TUB
SCGB1A1
BEST1
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
CSRP3
PDHX
BBOX1
PPFIBP2
SLC43A1
IFITM1
DGKZ
CHST1
API5
MADD
OR6A2
DCHS1
EIF3F
BRSK2
SYT7
SLC6A5
MTA2
UBE2L6
SNORD29
SNORD31
SNORD30
SNORD28
SNORD27
SNORD26
SNORD25
SNORD22
SLC22A6
SLC22A8
LPXN
PEX16
FADS2
MAPK8IP1
TP53I11
MICAL2
CTR9
ATG13
CKAP5
TRIM66
NR1H3
TSPAN32
TSSC4
USH1C
HIPK3
PRMT3
GLYAT
MRVI1
TRIM22
PRG3
IFITM3
SPON1
EIF3M
NXF1
DEAF1
IPO7
HTATIP2
IFITM2
TRIM3
TAF6L
SCGB1D2
SCGB1D1
CELF1
OR5I1
OR7E14P
OR7E12P
LYVE1
C11orf58
CLP1
KCNQ1OT1
PKP3
HPS5
PTGDR2
RRAS2
ZP1
SWAP70
GANAB
DTX4
DENND5A
NUP160
FNBP4
RRP8
SIRT3
OR52A1
SNHG1
ARFIP2
MTCH2
FJX1
C11orf41
ABTB2
PAMR1
ZDHHC5
DAK
DKFZP434K028
B3GAT3
FBXO3
SERGEF
EHF
OR5L2
OR5E1P
OR10A3
FXC1
TIMM10
BSCL2
ELP4
DKK3
RBMXL2
PGAP2
PRPF19
SLC43A3
COMMD9
C11orf21
PACSIN3
TRPM5
UBQLN3
RNF141
UBXN1
APIP
TMX2
HSD17B12
IGF2-AS1
TMEM216
BET1L
CEND1
SLC15A3
PHF21A
MS4A4A
WT1-AS
TMEM138
CYB5R2
TRIM34
CDHR5
TOLLIP
ZDHHC13
WDR74
TRIM44
MS4A12
MRPL16
SDHAF2
TMEM132A
HRASLS2
USP47
VPS37C
TRIM68
NAT10
UEVLD
LIN7C
SLC35C1
TCP11L1
LGR4
PIDD
KCNQ1DN
SOX6
AMBRA1
KBTBD4
PARVA
TTC17
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
PRDM11
CHRNA10
SLC17A6
PNPLA2
SYT13
PHRF1
LRRC4C
SCUBE2
MS4A7
ZBED5
SIGIRR
ALX4
RIC8A
MRPL17
FAM111A
ANO3
MS4A6A
MS4A5
EPS8L2
TUT1
STK33
CHID1
AHNAK
PRRG4
TMEM223
TMEM109
CCDC86
C11orf48
C11orf49
TRIM48
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
E2F8
SLC25A22
ZNF408
QSER1
AGBL2
ZBTB3
CPSF7
PRR5L
ASRGL1
ATHL1
INTS5
ZFP91
OR8J3
OR51G2
OR51E2
OR4P4
OR4C15
OR4A5
OR4A16
OR4A15
OR10W1
OR10V2P
PTDSS2
MOB2
SBF2
KIF18A
MS4A8B
FAM160A2
FAR1
BTBD10
ARFGAP2
ACCS
MS4A14
SPRYD5
PTPN5
MICALCL
LGALS12
TRIM5
TNKS1BP1
NAV2
SYT8
TSPAN18
CCDC34
SLC39A13
DEPDC7
GLYATL1
PRKCDBP
RPLP0P2
SAAL1
ODF3
SLC22A9
OSBPL5
C1QTNF4
PTPMT1
LRRC56
MRGPRE
ART5
MRGPRX2
MRGPRX3
MRGPRX4
HRASLS5
TRIM78P
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
C11orf74
OR4C46
OR4X2
OR4B1
OR52M1
OR52K2
OR5P2
OR5P3
GYLTL1B
CYP2R1
DBX1
DNAJC24
C11orf46
OR8I2
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
LOC120824
SYT9
LDLRAD3
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
MUC15
LOC143666
C11orf94
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
SLC5A12
LDHAL6A
C11orf42
NLRP6
NS3BP
METTL15
IMMP1L
OR56B4
ANO5
OR8U1
OR4C16
OR4C11
OR4S2
OR4C6
OR5D14
OR5L1
OR5D18
OR7E5P
OR5AS1
OR8K5
OR5T2
OR8H1
OR8K3
OR8J1
OR5R1
OR5M3
OR5M8
OR5M11
OR5AR1
OR5AK4P
LRRC55
SMTNL1
YPEL4
MED19
OR6Q1
OR9I1
OR9Q1
OR9Q2
OR1S2
OR1S1
OR10Q1
OR5B17
OR5B21
GLYATL2
MPEG1
OR5A2
OR5A1
OR4D6
OR4D11
PATL1
PLAC1L
MS4A15
VWCE
CYBASC3
PPP1R32
LRRN4CL
HNRNPUL2
ALKBH3
LOC221122
MS4A6E
LOC255512
OR52B2
OR4C3
OR4S1
C11orf35
EML3
OR51F1
SVIP
MRGPRX1
C11orf31
OR51B5
OR10AG1
OR5J2
OR4C13
OR4C12
KRT8P41
LOC283104
CSNK2A1P
OR51V1
LOC283116
H19
OR9G4
LOC283194
LINC00301
EFCAB4A
TMEM80
TTC9C
SLC22A24
HARBI1
LINC00294
IGSF22
OR10A4
OLFML1
LOC283299
C11orf36
NLRP10
NLRP14
ANO9
LUZP2
LOC338651
OR5F1
OR5AP2
B4GALNT4
LOC338739
OR52L1
OR2AG2
OR52B6
DCDC1
MS4A10
OR10A2
OVCH2
PDDC1
RTN4RL2
GALNTL4
B7H6
DKFZp779M0652
FAM111B
TMEM179B
ZFP91-CNTF
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
SLC22A25
IFITM5
FAM99A
OR56B1
GVINP1
INSC
FIBIN
C11orf96
SLC22A10
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
ACCSL
OR4X1
OR5D13
OR5D16
OR5W2
OR8H2
OR8H3
OR5T3
OR5T1
OR8K1
OR5M9
OR5M10
OR5M1
OR9G1
OR5AK2
OR5B2
OR5B12
OR5AN1
OR4D10
OR4D9
OR10V1
LRRC10B
NAV2-AS4
HNRNPKP3
FAM180B
OR51T1
OR51A4
OR51A2
IFITM10
OR4A47
OR4C45
SCGB1D4
MIR129-2
MIR130A
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440028
DKFZp686K1684
LOC440040
LOC440041
LOC441601
OR5B3
TRIM6-TRIM34
CCDC73
LOC494141
BDNF-AS1
MS4A13
OR8U8
OR9G9
MIR483
SNORA3
SNORA52
BTBD18
PGA3
PGA4
LOC644656
RASSF10
TRIM64C
LOC646813
LOC650368
LOC653486
SNORA23
SNORA45
SNORA54
SNORD67
SNORA57
SNORD97
MIR610
MIR611
INS-IGF2
MUC5B
LOC729013
LOC729799
METTL12
C11orf83
MIR675
LOC100126784
MRVI1-AS1
C11orf91
FAM99B
LOC100133161
MRPL23-AS1
MIR1908
MIR670
MIR3160-2
MIR3160-1
MIR3162
MIR4298
MIR4299
MTRNR2L8
MIR3654
MIR3680-1
LOC100500938
MIR210HG
LOC100506305
LOC100506540
DCDC5
LOC100507205
LOC100507300
LOC100507401
TMX2-CTNND1
SAA2-SAA4
HNRNPUL2-BSCL2
MIR4486
MIR4686
MIR4485
MIR3973
MIR4688
MIR4694
MIR1343
MIR4687
MIR4488

Genes in Wide Peak

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

Table S52. Genes in bold are cancer genes as defined by The Sanger Institute's 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 22q13.32.

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

Genes
hsa-mir-3201
hsa-let-7b
hsa-mir-1249
ACR
ARSA
CHKB
CPT1B
TYMP
FBLN1
PPARA
MAPK11
MAPK12
SBF1
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
GRAMD4
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
ATXN10
FAM19A5
RIBC2
SMC1B
NCAPH2
GTSE1
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
PANX2
CERK
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
SHANK3
TUBGCP6
LOC90834
LMF2
PHF21B
KLHDC7B
LOC150381
C22orf40
CN5H6.4
LOC284933
RPL23AP82
LOC339685
C22orf34
CHKB-CPT1B
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
FAM116B
PIM3
ODF3B
PRR5-ARHGAP8
SYCE3
LOC730668
LOC100128946
LOC100144603
LOC100271722
MIR1249
MIR3201
MIR3619
LOC100506714
MIR4763
MIR4762
MIR4535

Genes in Wide Peak

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

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

Genes
hsa-mir-339
GPER
NUDT1
PDGFA
PRKAR1B
MAFK
MAD1L1
EIF3B
ADAP1
SUN1
INTS1
SNX8
FTSJ2
GET4
CYP2W1
HEATR2
CHST12
FAM20C
MICALL2
PSMG3
C7orf50
ZFAND2A
COX19
KIAA1908
GPR146
TMEM184A
TFAMP1
UNCX
ELFN1
FLJ44511
LOC442497
MIR339
LOC100288524
MIR4655

Genes in Wide Peak

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

Table S55. 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 3p14.2.

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

Genes
FHIT
MITF
FOXP1
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
ARF4
DNASE1L3
EPHA3
FLNB
GBE1
GPR27
HTR1F
CNTN3
PDHB
POU1F1
PTPRG
ROBO1
ROBO2
ATXN7
TMF1
SLMAP
ACOX2
CGGBP1
CADPS
SUCLG2
HESX1
UBA3
MAGI1
PSMD6
ARL6IP5
RPP14
FAM107A
PDZRN3
FRMD4B
FAM208A
RYBP
CHMP2B
LRIG1
APPL1
ARHGEF3
IL17RD
PXK
FEZF2
EBLN2
SHQ1
ZNF654
LMOD3
ADAMTS9
ABHD6
C3orf14
PROK2
THOC7
ID2B
KBTBD8
SLC25A26
FAM3D
C3orf49
SNTN
SYNPR
ASB14
FAM19A4
PPP4R2
PRICKLE2
C3orf67
KCTD6
LOC201617
DNAH12
PDE12
FAM116A
CADM2
C3orf64
C3orf38
CCDC66
LOC285401
EIF4E3
SPATA12
VGLL3
LOC401074
FAM19A1
LOC440970
FLJ20518
FAM86DP
MIR548A2
GXYLT2
ZNF717
LOC100287879
FRG2C
MIR1284
MIR1324
MIR3136
MIR4272
MIR4273
LOC100506994
LOC100507062
ADAMTS9-AS2
MIR4795
MIR4444-1
LOC100652759

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.31.

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

Genes
PAX7
RPL22
SDHB
TNFRSF14
PRDM16
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
CORT
DDOST
DFFA
DFFB
DVL1
ECE1
MEGF6
EPHA2
ENO1
EPHA8
EPHB2
MTOR
GABRD
GNB1
ZBTB48
HSPG2
HTR1D
HTR6
TNFRSF9
MFAP2
MTHFR
NBL1
NPPA
NPPB
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PRKCZ
RAP1GAP
RSC1A1
SCNN1D
SKI
SLC2A5
SRM
TCEA3
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
UTS2
RER1
MST1P2
MST1P9
PADI2
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
NBPF1
NECAP2
DNAJC11
RCC2
AJAP1
CTNNBIP1
AGTRAP
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
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4684
MIR4689
MIR4632
MIR4417

Genes in Wide Peak

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

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

Genes
hsa-mir-596
CLN8
MYOM2
DLGAP2
ARHGEF10
KBTBD11
FBXO25
CSMD1
C8orf42
ERICH1
ZNF596
LOC286083
OR4F21
RPL23AP53
MIR596

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q24.2.

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

Genes
CBL
FLI1
ARHGEF12
hsa-mir-3167
hsa-mir-100
ACRV1
APLP2
CHEK1
DPAGT1
ETS1
GRIK4
H2AFX
HMBS
HSPA8
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
NFRKB
NRGN
OPCML
PVRL1
SC5DL
ST3GAL4
SORL1
SRPR
ST14
TECTA
THY1
ZNF202
BARX2
USP2
EI24
FEZ1
ARHGAP32
C2CD2L
ADAMTS8
IGSF9B
NCAPD3
VSIG2
TRIM29
POU2F3
HINFP
OR8G2
OR8B8
OR8G1
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
SPA17
SIAE
ROBO4
FOXRED1
SCN3B
CRTAM
PRDM10
GRAMD1B
PKNOX2
TP53AIP1
ABCG4
ROBO3
RNF26
FAM118B
NLRX1
C11orf61
CLMP
PDZD3
C11orf63
CCDC15
PUS3
MFRP
JAM3
KIRREL3
RPUSD4
TBRG1
UBASH3B
GLB1L2
ESAM
VPS26B
GLB1L3
TIRAP
C1QTNF5
PANX3
TMEM45B
PATE1
ADAMTS15
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
HEPACAM
OAF
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
TMEM225
OR8D4
LOC341056
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
BLID
LINC00167
HEPN1
LOC649133
LOC100128239
PATE3
MIR3167
LOC100499227
LOC100507392
MIR4697
MIR4493

Genes in Wide Peak

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

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

Genes
CDH7
CYB5A
GALR1
MBP
NFATC1
ZNF236
CTDP1
SOCS6
ZNF516
TSHZ1
CD226
TXNL4A
ADNP2
RTTN
KCNG2
SALL3
CDH19
TIMM21
TMX3
ZNF407
CNDP2
CCDC102B
RBFA
PQLC1
NETO1
PARD6G
CNDP1
DSEL
FAM69C
CBLN2
FBXO15
DOK6
ZADH2
C18orf62
LOC284276
LOC339298
ATP9B
LOC400655
LOC400657
HSBP1L1
LOC643542
C18orf63
LOC100130522
LOC100131655
LOC100505776
LOC100505817

Genes in Wide Peak

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

Table S61. 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 22q12.1.

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

Genes
ZNRF3

Genes in Wide Peak

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

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

Genes
BUB1B
C15orf55
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
ACTC1
B2M
CAPN3
CHRM5
CHRNA7
CKMT1B
EPB42
GANC
GATM
GCHFR
PDIA3
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
PLCB2
RAD51
RYR3
SCG5
SORD
SPINT1
SRP14
THBS1
TP53BP1
TYRO3
SLC30A4
EIF3J
JMJD7-PLA2G4B
SNAP23
SLC28A2
TGM5
PPIP5K1
AQR
ARHGAP11A
LCMT2
SLC12A6
RASGRP1
SERF2
GPR176
CHP
OIP5
BAHD1
MAPKBP1
GOLGA8A
RTF1
MGA
VPS39
CCNDBP1
C15orf63
TMEM87A
RPAP1
PLDN
GREM1
RPUSD2
TUBGCP4
EHD4
DUOX2
NDUFAF1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
DUOX1
DLL4
INO80
PPP1R14D
ZNF770
HAUS2
FAM82A2
DNAJC17
NOP10
C15orf24
PAK6
CASC5
AVEN
GJD2
STARD9
VPS18
SQRDL
ZFP106
SPATA5L1
CHAC1
C15orf29
WDR76
TMEM62
SPG11
ELL3
C15orf48
C15orf41
ZFYVE19
FRMD5
DISP2
ULK4P3
ULK4P1
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
CHST14
CASC4
TGM7
CATSPER2
PLA2G4E
TRIM69
C15orf43
LOC145663
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
HMGN2P46
LOC283710
FAM98B
PLA2G4D
FMN1
MRPL42P5
C15orf52
C15orf53
C15orf54
DUOXA2
GOLGA8B
EIF2AK4
CATSPER2P1
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
MIR626
MIR627
ANP32AP1
LOC728758
OIP5-AS1
MIR147B
LOC100131089
ANKRD63
JMJD7
PLA2G4B
ULK4P2
LOC100288615
MIR1233-1
MIR1282
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
MIR4510
TMCO5B

Genes in Wide Peak

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

Table S64. Genes in bold are cancer genes as defined by The Sanger Institute's 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
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 4p16.3.

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

Genes
hsa-mir-571
ATP5I
CTBP1
DGKQ
GAK
IDUA
MYL5
PDE6B
ZNF141
MAEA
PCGF3
SPON2
CPLX1
SLC26A1
FGFRL1
PIGG
KIAA1530
ABCA11P
MFSD7
TMEM175
C4orf42
ZNF595
ZNF721
ZNF718
CRIPAK
RNF212
ZNF876P
ZNF732
LOC100129917
LOC100130872
TMED11P

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17p13.3.

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

Genes
hsa-mir-22
hsa-mir-3183
ABR
CRK
MYO1C
PITPNA
SERPINF2
YWHAE
DOC2B
SCARF1
RPH3AL
PRPF8
TIMM22
GEMIN4
GLOD4
INPP5K
RNMTL1
VPS53
NXN
FAM57A
RILP
MIR22HG
SLC43A2
WDR81
TUSC5
FAM101B
C17orf97
MIR22
BHLHA9
TLCD2
DBIL5P
LOC100306951
MIR3183
LOC100506388

Genes in Wide Peak

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

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

Genes
BCL7A
hsa-mir-4304
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
ACADS
SCARB1
COX6A1
DTX1
EIF2B1
STX2
GOLGA3
GTF2H3
HPD
MMP17
MSI1
NOS1
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PLA2G1B
POLE
PRKAB1
PSMD9
PXMP2
PXN
RAN
RFC5
RPLP0
CLIP1
SFSWAP
TBX5
TBX3
HNF1A
UBC
ZNF10
ZNF26
ZNF84
ZNF140
CDK2AP1
ULK1
RASAL1
DENR
OASL
DYNLL1
SRSF9
HRK
HCAR3
HIP1R
PIWIL1
CABP1
NCOR2
KNTC1
MLEC
RBM19
RNF10
MPHOSPH9
CAMKK2
ZNF268
TMED2
GCN1L1
SDS
RAB35
SNRNP35
CIT
FZD10
MLXIP
RPH3A
P2RX2
FBXO21
SETD1B
ANKLE2
MED13L
SIRT4
ABCB9
RIMBP2
ATP6V0A2
FBXW8
HSPB8
HCAR1
GALNT9
ARL6IP4
TAOK3
POP5
ANAPC5
TRIAP1
TPCN1
RHOF
VSIG10
TESC
SBNO1
ZCCHC8
CHFR
WSB2
DIABLO
PITPNM2
EP400
DHX37
FBRSL1
DDX55
LHX5
SUDS3
C12orf43
VPS33A
RSRC2
AACS
DDX54
NOC4L
B3GNT4
OGFOD2
VPS37B
C12orf49
TCTN2
SLC24A6
RNF34
CCDC92
PUS1
COQ5
SRRM4
CCDC62
KDM2B
UNC119B
ORAI1
RNFT2
C12orf52
C12orf65
TMEM132C
CCDC64
SDSL
TMEM132B
IQCD
LOC116437
TMEM132D
SLC15A4
SPPL3
BRI3BP
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
LOC144742
CCDC60
PGAM5
RILPL2
DNAH10
PLBD2
LRRC43
LOC255480
GPR133
MORN3
KSR2
GATC
HNF1A-AS1
DDX51
HCAR2
LOC338799
EP400NL
RILPL1
IL31
CCDC42B
TMEM233
SETD8
LOC387895
LOC400084
FLJ37505
LOC440117
FLJ31485
MAP1LC3B2
LOC647589
SNORA49
MIR620
LOC100128554
LOC100130238
LOC100190940
LINC00173
ZNF605
MIR1178
MIR4304
MIR3612
MIR3908
LOC100506649
LOC100506668
LOC100507055
LOC100507066
LOC100507091
LOC100507206
ZNF664-FAM101A
MIR4498
MIR4472-2
MIR4700

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p11.22.

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

Genes
FGFR1
WHSC1L1
ADRB3
ADAM3A
EIF4EBP1
ADAM2
NRG1
IDO1
STAR
TACC1
ADAM18
ADAM9
ASH2L
BAG4
ERLIN2
PROSC
DDHD2
GPR124
LSM1
BRF2
C8orf4
PLEKHA2
DUSP26
RNF122
ZNF703
TTI2
RAB11FIP1
TM2D2
PPAPDC1B
MAK16
FUT10
GOT1L1
UNC5D
LETM2
KCNU1
IDO2
HTRA4
ADAM32
ADAM5P
RNF5P1
C8orf86
LOC728024
LOC100130964

Genes in Wide Peak

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

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

Genes
AUTS2

Genes in Wide Peak

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

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

Genes
PTPRD

Genes in Wide Peak

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

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

Genes
RB1
RCBTB2
LPAR6

Genes in Wide Peak

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

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

Genes
DLG2
TMEM126B

Genes in Wide Peak

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

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

Genes
CREBBP
DNASE1
TRAP1
CLUAP1
NAA60
SLX4
ZNF597
NLRC3
C16orf90

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q13.1.

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

Genes
NKX2-1
CCNB1IP1
hsa-mir-3172
hsa-mir-624
hsa-mir-3171
hsa-mir-4307
hsa-mir-208b
hsa-mir-1201
ANG
APEX1
ARHGAP5
BCL2L2
CEBPE
CFL2
CMA1
LTB4R
CTSG
DAD1
COCH
FOXG1
GPR33
GZMH
GZMB
FOXA1
HNRNPC
MMP14
MYH6
MYH7
NEDD8
NFATC4
NFKBIA
NOVA1
PNP
NRL
OXA1L
PAX9
PCK2
PRKD1
PSMA6
PSMB5
PSME1
PSME2
RABGGTA
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
SALL2
SRP54
SSTR1
TEP1
TGM1
PABPN1
AP1G2
SLC7A7
CPNE6
AKAP6
KIAA0391
TOX4
REC8
PARP2
DHRS2
EFS
IRF9
PRMT5
TM9SF1
EDDM3A
DHRS4
RIPK3
AP4S1
BAZ1A
SUPT16H
ACIN1
SCFD1
KHNYN
SLC7A8
HECTD1
HEATR5A
NGDN
LRP10
NKX2-8
TINF2
OR10G3
OR10G2
OR4E2
CIDEB
CHMP4A
STXBP6
STRN3
SLC39A2
FAM158A
ZNF219
GMPR2
SLC22A17
MBIP
HAUS4
PPP2R3C
C14orf119
RNF31
RBM23
C14orf167
G2E3
OSGEP
ARHGEF40
EAPP
METTL3
LTB4R2
SDR39U1
RPGRIP1
NDRG2
NYNRIN
HOMEZ
CHD8
SNX6
C14orf93
ABHD4
NPAS3
EDDM3B
CDH24
METTL17
IL25
THTPA
OR4K5
OR11H2
OR4K1
IPO4
NUBPL
DCAF11
OR4K15
BRMS1L
JPH4
RNASE7
INSM2
ARHGAP5-AS1
RAB2B
AJUBA
ZFHX2
RPPH1
SLC25A21
LRRC16B
PPP1R3E
TMEM55B
TTC5
EGLN3
C14orf126
DHRS1
CMTM5
RNASE11
TPPP2
RNASE8
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
KLHL33
MIPOL1
MDP1
CLEC14A
FITM1
REM2
C14orf21
SPTSSA
ADCY4
RALGAPA1
SFTA3
IGBP1P1
LOC283624
TSSK4
FAM177A1
DHRS4L2
SNORD8
RNASE10
OR6S1
C14orf23
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
POTEG
MIR208A
C14orf165
OR11H12
RNASE13
OR4Q3
OR4M1
RNASE12
POTEM
LOC642426
ECRP
C14orf176
CBLN3
SNORD9
MIR624
DHRS4L1
SNORD126
MIR208B
LOC100129794
MIR4307
LOC100505967
LOC100506071
NEDD8-MDP1
BCL2L2-PABPN1
MIR4503
MIR548AI
MIR4707

Genes in Wide Peak

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

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

Genes
ATIC
ACSL3
PAX3
FEV
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
hsa-mir-26b
hsa-mir-548f-2
AAMP
ACADL
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CPS1
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
ERBB4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
MAP2
MYL1
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SNORD20
RPE
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
XRCC5
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
LANCL1
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
CPS1-IT1
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ACCN4
DOCK10
MREG
PECR
C2orf83
MFF
CXCR7
RNPEPL1
MARCH4
WDFY1
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
PKI55
C2orf67
LOC151171
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
TIGD1
LOC200772
CCDC108
C2orf72
CXXC11
UNC80
RUFY4
DUSP28
ESPNL
ECEL1P2
LOC348761
C2orf62
RBM44
AQP12A
KLHL30
RESP18
C2orf82
OR6B2
ASB18
FLJ43879
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
LOC646324
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
LOC100129175
PP14571
LOC100130451
LOC100286922
MIR1471
MIR1244-1
MIR548F2
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3132
MIR4269
UBE2F-SCLY
MIR4439
MIR4776-1
MIR4777
MIR2467
MIR4440
MIR4786
MIR4776-2
MIR4441

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q21.2.

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

Genes
CCDC6

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20q13.12.

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

Genes
MIR3616

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q34.11.

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

Genes
ABL1
NOTCH1
RALGDS
SET
TSC1
BRD3
NUP214
FNBP1
hsa-mir-602
hsa-mir-4292
hsa-mir-126
hsa-mir-219-2
hsa-mir-3154
hsa-mir-2861
hsa-mir-181b-2
hsa-mir-601
hsa-mir-600
hsa-mir-147
ABCA2
ABO
AK1
ASS1
C5
C8G
CACNA1B
CCBL1
ENTPD2
CDK9
CEL
CELP
COL5A1
CRAT
DBC1
DBH
SARDH
DNM1
TOR1A
MEGF9
ENDOG
ENG
STOM
FCN1
FCN2
FPGS
NR5A1
FUT7
NR6A1
GGTA1P
GLE1
GOLGA1
GOLGA2
GPR21
RAPGEF1
GRIN1
GSN
HSPA5
LCN1
LCN2
LMX1B
NDUFA8
ODF2
PAEP
PAPPA
PDCL
PBX3
PPP2R4
PPP6C
PSMB7
PSMD5
PTGDS
PTGS1
RPL7A
RPL12
RXRA
SNAPC4
SPTAN1
STXBP1
SURF1
SURF2
SURF4
MED22
SURF6
TLR4
TRAF1
TRAF2
TTF1
VAV2
ZNF79
LHX3
GFI1B
SSNA1
EDF1
DPM2
FUBP3
CLIC3
GTF3C5
GTF3C4
LHX2
MED27
PTGES
RALGPS1
ADAMTSL2
PPP1R26
SEC16A
SH2D3C
RABEPK
LAMC3
TUBB4B
UBAC1
OLFM1
ZER1
AGPAT2
POMT1
ZBTB6
NEK6
SDCCAG3
NOXA1
USP20
SLC27A4
CNTRL
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
RPL35
MAN1B1
DOLK
TRIM32
SETX
ZBTB43
PMPCA
ASTN2
EXOSC2
NCS1
ANGPTL2
NUP188
RABGAP1
CIZ1
COBRA1
NELF
GPSM1
DKFZP434A062
GAPVD1
PHF19
FBXW2
OR1J4
GBGT1
LHX6
OR1L3
OR1L1
OR1J2
SNORA65
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
TRUB2
ST6GALNAC4
NDOR1
TOR1B
TOR2A
METTL11A
PHPT1
ANAPC2
PKN3
DPP7
SLC2A8
OBP2B
OBP2A
ST6GALNAC6
MRPS2
COQ4
CERCAM
EGFL7
PRRX2
C9orf114
RAB14
C9orf78
FBXW5
RC3H2
TBC1D13
C9orf167
EXD3
STRBP
C9orf86
CDK5RAP2
LRRC8A
INPP5E
NPDC1
BARHL1
SH3GLB2
REXO4
DOLPP1
KCNT1
ZBTB26
DENND1A
GPR107
LINC00474
PRDM12
CARD9
DDX31
FAM129B
MRPL41
C9orf16
MAPKAP1
EHMT1
PTGES2
MIR600HG
URM1
ARPC5L
AIF1L
UCK1
GARNL3
NTNG2
PRRC2B
PPAPDC3
ZDHHC12
FAM73B
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
FAM125B
WDR34
SAPCD2
C9orf69
LRSAM1
UAP1L1
MRRF
RBM18
ARRDC1
WDR85
TMEM203
SLC25A25
ZMYND19
NACC2
C9orf116
LCN8
FAM69B
PTRH1
PIP5KL1
OR1L8
OR1N2
OR1N1
ASB6
SLC34A3
DAB2IP
CAMSAP1
C9orf163
MAMDC4
LCN6
AK8
OR1Q1
TTLL11
TTC16
C9orf96
OLFML2A
QSOX2
NAIF1
LOC253039
PHYHD1
MORN5
OR1L4
LINC00094
CRB2
SCAI
C9orf117
LCN12
C9orf142
TPRN
FAM78A
GPR144
QRFP
OR1J1
OR1B1
GLT6D1
SWI5
C9orf50
PNPLA7
C9orf169
ENTPD8
LOC389791
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
OR1L6
OR5C1
OR1K1
LCN9
FAM102A
WDR38
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
ZBTB34
MIR126
MIR147A
MIR181A2
MIR181B2
MIR199B
MIR219-2
C9orf106
LCN10
C9orf173
NRARP
NRON
FAM163B
FLJ40292
TUBBP5
RNF224
SNORA17
SNORA43
SNORD62B
SNORD90
MIR600
MIR601
MIR602
RNF208
DNLZ
SNORA70C
LOC100128505
LOC100128593
LOC100129034
LOC100129722
LOC100130954
LOC100131193
FAM157B
RNU6ATAC
LOC100272217
LOC100288842
LOC100289019
LOC100289341
MIR181A2HG
MIR4292
MIR3154
MIR2861
MIR3621
MIR3689A
MIR3911
MIR3689B
LOC100506100
LOC100506190
LOC100506599
MIR3689D1
MIR3689F
MIR4669
MIR4673
MIR3960
MIR4674
MIR4478
MIR3689C
MIR2964A
MIR3689D2
MIR4672
MIR3689E
MIR4479

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q23.

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

Genes
BLM
IDH2
NTRK3
PML
CRTC3
hsa-mir-1469
hsa-mir-3175
hsa-mir-3174
hsa-mir-9-3
hsa-mir-7-2
hsa-mir-1276
hsa-mir-549
hsa-mir-184
hsa-mir-4313
hsa-mir-631
hsa-mir-630
ACAN
ALDH1A3
ANPEP
BBS4
BCL2A1
BNC1
CHD2
CHRNA3
CHRNA5
CHRNB4
CLK3
CRABP1
CSK
CSPG4
CTSH
CYP1A1
CYP1A2
CYP11A1
ETFA
FAH
FES
HEXA
IDH3A
IGF1R
IL16
IREB2
ISG20
ISLR
LOXL1
MAN2A2
MAN2C1
MEF2A
MFGE8
MPI
MYO9A
NEO1
NMB
FURIN
PDE8A
PKM2
PLIN1
POLG
PSMA4
PTPN9
RASGRF1
RCN2
RLBP1
RPS17
SH3GL3
NR2F2
TYRO3P
AP3B2
ST8SIA2
SEMA7A
PEX11A
IQGAP1
PSTPIP1
PRC1
SLC28A1
COX5A
STOML1
HOMER2
ZNF592
SV2B
ARNT2
NR2E3
HCN4
SCAMP2
SNUPN
TSPAN3
AP3S2
HMG20A
SEMA4B
CIB2
CIB1
MTHFS
ARID3B
MORF4L1
ABHD2
ADAMTS7
AKAP13
TBC1D2B
MESDC2
ACSBG1
KIAA1024
SYNM
TMED3
SEC11A
GABARAPL3
ARIH1
SIN3A
ULK3
FBXO22
VPS33B
MRPL46
NPTN
SLCO3A1
SCAPER
HDGFRP3
NGRN
RHCG
BTBD1
TM6SF1
ZFAND6
SCAND2
LRRC49
RPP25
COMMD4
ZSCAN2
DET1
LINS
FANCI
IMP3
DNAJA4
MCTP2
GOLGA6B
MESP1
UNC45A
C15orf39
RGMA
WDR93
PARP6
C15orf17
ADAMTSL3
KIAA1199
ALPK3
ISLR2
FAM108C1
MESDC1
PPCDC
CELF6
STRA6
KLHL25
CPEB1
AEN
ISL2
TTC23
MRPS11
EFTUD1
NEIL1
LRRK1
LMAN1L
PEAK1
THSD4
C15orf34
CCDC33
EDC3
AGSK1
WDR61
CD276
STARD5
C15orf5
ADPGK
FAM103A1
MEX3B
LINGO1
WDR73
UBL7
C15orf42
RCCD1
LOC91450
ARRDC4
LOC91948
UBE2Q2
C15orf40
SENP8
HIGD2B
LRRC28
C15orf27
AGBL1
AGPHD1
WHAMM
FSD2
ASB7
LYSMD4
PGPEP1L
LOC145820
C15orf32
HAPLN3
MESP2
SPATA8
NRG4
LINC00052
C15orf26
TBC1D21
ODF3L1
ADAMTS17
SCAMP5
DNM1P46
CT62
GRAMD2
CERS3
LOC253044
LOC254559
SNX33
C15orf60
C15orf37
LOC283688
LOC283692
LOC283693
FAM154B
LOC283731
LOC283738
LOC283761
FAM169B
TMEM202
LOC338963
GOLGA6A
TMC3
ZNF774
C15orf38
GOLGA6L5
KIF7
ZNF710
HDDC3
C15orf59
LOC388152
UBE2Q2P1
FLJ42289
ANKRD34C
C15orf58
LOC390660
ST20
FAM174B
LOC400456
MIR184
MIR7-2
MIR9-3
LOC440288
GOLGA6L9
LOC440297
DNM1P41
LOC440300
TTLL13
CPLX3
LOC645752
SH2D7
LOC646938
GOLGA6L10
LOC648809
GOLGA6C
GOLGA6D
SCARNA15
FBXO22-AS1
MIR549
MIR630
MIR631
LOC727849
LOC727915
ASB9P1
LOC729739
LOC729911
DNM1P35
UBE2Q2P3
UBE2Q2P2
LOC100144604
LOC100287559
LOC100287616
MIR1276
MIR1179
MIR1469
MIR3175
MIR4313
RPS17L
LOC100505679
LOC100506874
LOC100507217
C15orf38-AP3S2
ST20-MTHFS
MIR4514
MIR4513
MIR3529
MIR4515
MIR4714

Genes in Wide Peak

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

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

Genes
hsa-mir-33b
SREBF1
TOM1L2
MIR33B

Genes in Wide Peak

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

Table S81. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BRCA2
CDX2
FLT3
LCP1
LHFP
TTL
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
CDK8
CPB2
ELF1
FGF9
FOXO1
FLT1
GJA3
GJB2
GPR12
GTF2F2
GTF3A
HMGB1
PDX1
MAB21L1
SMAD9
MIPEP
PABPC3
UBL3
RFC3
RFXAP
RNF6
RPL21
SGCG
SLC7A1
TPT1
TRPC4
TUBA3C
ZMYM2
IFT88
TNFSF11
TSC22D1
CCNA1
MTMR6
DCLK1
ZMYM5
KL
MTRF1
NUPL1
FRY
SLC25A15
USPL1
MRPS31
SAP18
N4BP2L2
POSTN
GJB6
HSPH1
WASF3
WBP4
AKAP11
EXOSC8
PDS5B
KIAA0564
ZC3H13
SPG20
LRCH1
MTUS2
SACS
LATS2
NUFIP1
SNORD102
NBEA
C13orf15
DNAJC15
ALG5
POLR1D
CRYL1
POMP
UFM1
ATP8A2
IL17D
MPHOSPH8
SOHLH2
ENOX1
PSPC1
KIAA1704
TNFRSF19
FAM48A
CENPJ
RNF17
COG6
XPO4
MRP63
NAA16
KIAA0226L
PROSER1
COG3
KATNAL1
KBTBD7
C13orf33
KBTBD6
STARD13
N4BP2L1
TPTE2
EPSTI1
CG030
LINC00284
CSNK1A1L
RXFP2
TEX26
FAM216B
LACC1
LINC00330
B3GALTL
DGKH
CCDC122
STOML3
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
PHF2P1
SUGT1P3
SIAH3
SLC46A3
ANKRD20A9P
C1QTNF9
FREM2
LINC00442
TPTE2P6
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
ATP5EP2
LOC440131
C1QTNF9B-AS1
SNORA27
TSC22D1-AS1
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
SNORA31
MIR621
CCDC169
ANKRD26P3
RPL21P28
LINC00426
TPT1-AS1
LINC00421
PAN3-AS1
MIR548F5
MIR2276
MIR320D1
MIR4305
LINC00327
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
MIR4499
LOC100616668

Genes in Wide Peak

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

Table S82. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
AKT2
BCL3
CD79A
ERCC2
KLK2
PPP2R1A
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
A1BG
ACTN4
AP2A1
APOC1
APOC1P1
APOC2
APOC4
APOE
KLK3
ATP1A3
AXL
BAX
BCAT2
BCKDHA
CEACAM1
BLVRB
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CEACAM5
CGB
CEACAM3
CEACAM7
CEACAM8
CEACAM4
CKM
AP2S1
CLC
CLPTM1
CRX
CYP2A6
CYP2A7
CYP2A13
CYP2B6
CYP2B7P1
CYP2F1
DBP
DMPK
DMWD
ECH1
MEGF8
EMP3
ERCC1
ERF
FBL
ETFB
FCAR
FCGRT
FKBP1AP1
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GIPR
GPR4
GPR32
GRIK5
GRIN2D
ARHGAP35
GSK3A
GYS1
HAS1
FOXA3
HNRNPL
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KCNN4
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LGALS4
LGALS7
LHB
LIG1
LIM2
LIPE
BCAM
MAP3K10
MYBPC2
CEACAM6
NDUFA3
NFKBIB
NKG7
CNOT3
NOVA2
NPAS1
NTF4
NUCB1
PAFAH1B3
PEG3
PLAUR
POLD1
POU2F2
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PSMC4
PSMD8
PTGIR
PTPRH
PVR
PVRL2
RELB
RPL18
RPL28
MRPS12
RPS5
RPS9
RPS11
RPS16
RPS19
RRAS
RTN2
RYR1
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPA
SNRPD2
SPIB
AURKC
SULT2B1
SULT2A1
SUPT5H
SYT5
TGFB1
TNNI3
TNNT1
TULP2
NR1H2
VASP
XRCC1
ZFP36
ZNF8
ZNF17
ZNF28
MZF1
ZNF45
ZNF221
ZNF222
ZNF132
ZNF134
ZNF135
ZNF137P
ZNF154
ZNF155
ZNF175
ZNF180
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF230
SYMPK
MIA
DPF1
LTBP4
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
FCGBP
PGLYRP1
UBE2M
ARHGEF1
DYRK1B
NUMBL
CYTH2
ZNF235
ZNF264
KCNK6
NCR1
NAPSA
GMFG
KLK4
ZNF432
DHX34
SAE1
TRIM28
ZNF256
LILRB2
PAK4
TOMM40
ZNF211
RABAC1
TRAPPC2P1
SPINT2
DLL3
ZNF234
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
HNRNPUL1
CLASRP
KPTN
MAP4K1
KLK8
PNKP
U2AF2
ATF5
PPP6R1
CARD8
SIRT2
CYP2G1P
SIPA1L3
ZC3H4
FBXO46
ETHE1
RPL13A
SYNGR4
LILRA4
PRG1
ZIM2
NUP62
HSPBP1
PPP1R15A
PLD3
EML2
ZNF324
KLK5
PRKD2
ZNF473
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
ZNF285
SIGLEC7
LYPD3
BBC3
DKKL1
SIGLEC9
SIGLEC8
GPR77
CHMP2A
DHDH
ZNF544
EIF3K
UBE2S
SLC6A16
LGALS13
CYP2S1
STRN4
CCDC106
EPN1
SERTAD3
SERTAD1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF581
PTOV1
RAB4B
PAF1
PPP1R12C
TRPM4
ZNF586
QPCTL
FAM83E
EPS8L1
RASIP1
SARS2
TMEM160
PIH1D1
SAMD4B
ATP5SL
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
MED29
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
SMG9
IRGC
CABP5
SPHK2
LGALS14
EXOSC5
MEIS3
CEACAM19
SLC17A7
NAT14
CD177
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
LRFN1
USP29
PLEKHA4
PRX
SPTBN4
MARK4
CATSPERG
ZNF71
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
DMRTC2
C19orf33
ELSPBP1
LIN7B
HIF3A
ZNF574
PLEKHG2
ZNF649
ZSCAN18
MGC2752
TSEN34
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF576
ZNF329
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
ADCK4
CNTD2
ZNF702P
ZNF606
ZNF614
FUZ
OPA3
ITPKC
B9D2
RSPH6A
ZNF611
MED25
BCL2L12
TEX101
GRWD1
WDR87
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
CNFN
SNORD35B
ZNF347
ZNF577
SUV420H2
C19orf48
ZBTB45
ZNF587
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF551
CEACAM21
ZNF616
ZNF766
CCDC97
EXOC3L2
ZNF468
ZNF160
CTU1
ZNF835
YIF1B
ZNF765
NLRP12
MYADM
ZNF845
TIMM50
SHKBP1
CCDC114
DKFZp434J0226
ACPT
CGB5
CGB7
LRRC4B
LENG9
CGB8
GNG8
PPP1R14A
EGLN2
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
FBXO17
KIR3DL3
RASGRP4
ZNF526
ZNF837
CLDND2
ZNF816
ZNF543
CEACAM20
COX6B2
OSCAR
ZNF813
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZNF573
EID2B
IRGQ
ZNF428
RINL
FBXO27
C19orf47
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
NLRP4
ZNF542
ZNF582
ZNF583
FAM98C
CAPN12
LGALS16
TTC9B
CDC42EP5
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF296
DEDD2
ZNF579
ZNF114
EID2
ZNF780B
ZNF525
SPACA4
NLRP7
GGN
CADM4
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
VSTM1
TMEM150B
FAM71E2
VN1R2
VN1R4
NLRP9
ZNF546
MYPOP
NANOS2
NCCRP1
SYCN
LEUTX
ZNF404
ZNF284
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
SELV
ZNF530
C19orf51
ZNF233
LILRA5
B3GNT8
IGFL1
ZNF773
LOC386758
CEACAM22P
CEACAM16
BLOC1S3
LOC388553
IGFL3
ZNF808
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
PAPL
LOC390940
ZNF805
SPRED3
ZNF321P
LGALS17A
SIGLEC16
FLJ26850
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
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
TMEM91
LOC643669
LOC644554
LOC646508
SBK2
LOC646862
PSG10P
LGALS7B
PHLDB3
SEC1
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR641
MIR642A
MIR643
RPL13AP5
CCDC61
CEACAM18
SHISA7
FLJ30403
ZNF814
MIR769
SIGLEC14
MIMT1
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
LOC100128252
LOC100128398
LOC100129083
LOC100129935
SGK110
BSPH1
LOC100131691
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
LOC100287177
LOC100289650
ZNF587B
MIR1283-2
MIR1323
MIR1283-1
LOC100379224
MIR3191
MIR3190
MIR320E
MIR4324
MIR4323
MIR642B
LOC100505495
LOC100505622
LOC100505681
LOC100505715
LOC100505812
LOC100506012
LOC100506033
LOC100506068
LOC100507003
ZNF865
ZNF816-ZNF321P
MIA-RAB4B
RAB4B-EGLN2
APOC4-APOC2
MIR4530
MIR4754
MIR4752
MIR371B
MIR4749
MIR4750
MIR4531
MIR4751
LOC100631378

Genes in Wide Peak

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

Table S83. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CBFA2T3
CBFB
CDH1
CDH11
CYLD
FANCA
MAF
HERPUD1
hsa-mir-1910
hsa-mir-3182
hsa-mir-1972-2
hsa-mir-140
hsa-mir-1538
hsa-mir-328
hsa-mir-138-2
hsa-mir-3181
hsa-mir-1826
AARS
ADCY7
AP1G1
AFG3L1P
AGRP
AMFR
APRT
ZFHX3
BBS2
C16orf3
CA5A
CA7
CALB2
CBLN1
CDH3
CDH5
CDH8
CDH13
CDH15
CDH16
CES1
CETP
CNGB1
COX4I1
CSNK2A2
CTRB1
CTRL
CYBA
DHODH
NQO1
DYNC1LI2
DPEP1
E2F4
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GLG1
GNAO1
GOT2
HAS3
HP
HPR
HSBP1
HSD11B2
HSD17B2
HSF4
IRF8
KARS
KIFC3
LCAT
MC1R
CHST6
MMP2
MMP15
MT1A
MT1B
MT1E
MT1F
MT1G
MT1H
MT1JP
MT1M
MT1L
MT1X
MT2A
MT3
MVD
NFATC3
CHMP1A
PHKB
PLCG2
POLR2C
PSKH1
PSMB10
PSMD7
RBL2
RPL13
RRAD
SALL1
CCL17
CCL22
CX3CL1
SIAH1
ST3GAL2
SLC6A2
SLC9A5
SLC12A3
SLC12A4
SNTB2
SPG7
TAT
TERF2
TK2
ZNF19
ZNF23
GAN
SLC7A5
CDK10
TRADD
MBTPS1
CES2
NAE1
NOL3
TAF1C
SLC7A6
USP10
ATP6V0D1
GPR56
BCAR1
C16orf7
N4BP1
NUP93
KIAA0513
PIEZO1
DHX38
IST1
ATP2C2
CLEC3A
CHST4
MPHOSPH6
NUTF2
IRX5
DNAJA2
KATNB1
ZNF267
COX4NB
TUBB3
CFDP1
CTCF
NFAT5
NUDT21
WWP2
PRDM7
DDX19B
GABARAPL2
MON1B
TCF25
CNOT1
PHLPP2
ZNF423
ZCCHC14
KIAA0182
ATMIN
RPGRIP1L
COTL1
MLYCD
SF3B3
CES3
ADAT1
CHST5
ARL2BP
ORC6
EDC4
PLA2G15
TP53TG3
COG4
PLEKHG4
DKFZP434H168
LRRC29
CPNE7
VPS4A
IL17C
TOX3
NOB1
CCDC113
TMEM208
C16orf80
FHOD1
BRD7
ANKRD11
ZDHHC1
OSGIN1
PARD6A
PLLP
CKLF
NIP7
FAM96B
GINS2
TPPP3
TRAPPC2L
CES1P1
WWOX
BCMO1
TERF2IP
PRMT7
NECAB2
KLHDC4
HYDIN
DEF8
DUS2L
CHTF8
LPCAT2
TXNL4B
BANP
HEATR3
PDPR
RFWD3
SLC38A7
OGFOD1
LRRC36
DDX19A
FBXL8
SMPD3
ZNF821
ZDHHC7
VAC14
DOK4
VPS35
FTSJD1
DDX28
TSNAXIP1
CENPN
C16orf61
COQ9
CIAPIN1
THAP11
JPH3
PDP2
ZNF319
RANBP10
VAT1L
KIAA1609
WFDC1
NOD2
PDF
DPEP2
DPEP3
PAPD5
AKTIP
MTHFSD
GINS3
NDRG4
ACD
DBNDD1
FTO
FA2H
IRX6
IRX3
FAM65A
TMEM231
TMCO7
C16orf57
WDR59
ELMO3
KLHL36
FBXO31
SHCBP1
SETD6
ESRP2
FAM192A
CENPT
CHD9
C16orf70
CYB5B
CMIP
ITFG1
GFOD2
CDT1
MAP1LC3B
NETO2
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
LONP2
C16orf48
SLC7A6OS
NLRC5
CCDC135
CAPNS2
COG8
SPIRE2
MT4
ZNF469
GPT2
B3GNT9
CIRH1A
ZNRF1
ABCC11
NKD1
CNTNAP4
RSPRY1
MYLK3
MARVELD3
MTSS1L
CENPBD1
ZNF276
CCDC102A
KCNG4
SDR42E1
ABCC12
CMTM1
PKD1L2
RNF166
EXOSC6
C16orf46
DNAAF1
NRN1L
CMTM3
C16orf78
SPATA2L
C16orf55
ANKRD26P1
ZC3H18
CDYL2
SNX20
TMEM170A
SLC38A8
ZFP90
RLTPR
KCTD19
CMTM4
CMTM2
BEAN1
SLC22A31
IL34
TMED6
LOC146481
FLJ30679
LOC146513
ZFPM1
ADAD2
ZFP1
ADAMTS18
MGC23284
LINC00311
LDHD
FUK
MLKL
ZNF778
ACSF3
CPNE2
GPR114
PRSS54
CES5A
GPR97
CNEP1R1
CCDC79
CES4A
EXOC3L1
LOC283856
LINC00304
LOC283867
HTA
LOC283914
LOC283922
NUDT7
PDXDC2P
CLEC18C
MT1DP
SNAI3
FAM92B
ATXN1L
PKD1L3
CLEC18A
CTU2
TEPP
SLC6A10P
C16orf87
LOC388276
C16orf86
LOC390705
CES1P2
PABPN1L
FLJ26245
LOC400548
LOC400550
LOC400558
C16orf74
MIR138-2
MIR140
HERC2P4
CTRB2
MIR328
CLEC18B
SNORD68
UBE2MP1
LOC643714
LOC643802
CRNDE
MT1IP
LOC644649
LINC00273
KIAA0895L
TP53TG3C
SNORA46
SNORA50
SNORD71
SNORD111
LOC727710
LOC729264
TP53TG3B
LOC729513
LOC732275
SNORD111B
LOC100128881
LOC100129617
LOC100130015
LOC100130700
LOC100130894
SYCE1L
LOC100287036
MIR1538
MIR1972-1
MIR1910
SNORA70D
MIR3182
MIR1972-2
MIR3935
LOC100505619
LOC100505865
LOC100506083
LOC100506172
C16orf95
LOC100507577
CKLF-CMTM1
MIR4720
MIR4722
MIR4719
MIR548AE2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q21.2.

Table S84. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
BRCA1
ERBB2
ETV4
LASP1
MLLT6
RARA
TAF15
hsa-mir-1203
hsa-mir-152
hsa-mir-4315-1
hsa-mir-2117
hsa-mir-2909
ACACA
ACLY
AP2B1
AOC2
ARL4D
ATP6V0A1
FMNL1
CACNB1
CDC6
CDC27
CCR7
CNP
CRHR1
CSF3
DHX8
DUSP3
EZH1
GAST
FZD2
G6PC
KAT2A
GFAP
CCR10
GRB7
GRN
HCRT
HSD17B1
IFI35
IGFBP4
ITGA2B
ITGB3
JUP
KPNB1
KRT9
KRT10
KRT12
KRT13
KRT14
KRT15
KRT16
KRT17
KRT19
KRT31
KRT32
KRT33A
KRT33B
KRT34
KRT35
LHX1
LIG3
NBR1
MAPT
ADAM11
MEOX1
MPP2
MPP3
MYL4
NAGLU
NEUROD2
NFE2L1
NMT1
NSF
PEX12
PNMT
MED1
PPY
PSMB3
PYY
PSMD3
RAB5C
RAD51D
RPL19
RPL27
CCL1
CCL2
CCL3
CCL3L1
CCL4
CCL5
CCL7
CCL8
CCL11
CCL13
CCL14
CCL15
CCL16
CCL18
CCL23
SLC4A1
SMARCE1
SP2
STAT3
STAT5A
STAT5B
TADA2A
HNF1B
MLX
THRA
TOP2A
DNAJC7
TUBG1
UBTF
WNT3
WNT9B
PCGF2
RND2
PIP4K2B
CNTNAP1
TCAP
SKAP1
AOC3
BECN1
KRT38
KRT37
KRT36
HAP1
MAP3K14
ZNHIT3
EFTUD2
RPL23
NPEPPS
CCL4L1
GOSR2
NR1D1
TBKBP1
PLEKHM1
MED24
LRRC37A
HDAC5
GJC1
PSME3
EIF1
NBR2
RAMP2
VAT1
LEPREL4
HEXIM1
CCT6B
C1QL1
RUNDC3A
STARD3
CBX1
DDX52
DUSP14
SYNRG
CASC3
IKZF3
GPATCH8
KCNH4
FAM215A
KRT23
AATF
TUBG2
NKIRAS2
CCDC56
PSMC3IP
SNX11
TBX21
SOCS7
SOST
RAPGEFL1
COPZ2
ARL17A
SLC25A39
HIGD1B
CDK12
KRT20
NLE1
FNDC8
CWC25
LRRC37A4
SLFN12
PNPO
KLHL11
GSDMB
ATXN7L3
PLXDC1
LYZL6
ARHGAP23
FKBP10
WNK4
C17orf53
TMUB2
DHX58
MMP28
DHRS11
PRR15L
ACBD4
DCAKD
GGNBP2
MRM1
PLEKHH3
DBF4B
MYO19
CDK5RAP3
SP6
COASY
SRCIN1
AARSD1
KRTAP1-3
KRTAP1-1
KRTAP9-9
KRTAP4-6
KRTAP2-1
TTC25
KRTAP4-12
KRTAP1-5
KRTAP3-1
KRTAP3-2
KRTAP9-2
KRTAP9-3
KRTAP9-8
KRTAP17-1
PPP1R1B
TBC1D3F
MIEN1
MRPL45
VPS25
TMEM101
GHDC
KRTAP4-4
TNS4
FBXL20
KRTAP9-4
KRTAP4-1
KRTAP4-5
KRTAP4-3
KRTAP4-2
KRTAP3-3
KRTAP2-4
LRRC46
SCRN2
AOC4
ZNF830
SLFN11
RASL10B
G6PC3
ASB16
PGAP3
HSPB9
ORMDL3
PLCD3
TMEM106A
OSBPL7
NT5C3L
RFFL
ZPBP2
C17orf46
HEXIM2
LSM12
CCDC43
CNTD1
TMEM132E
C17orf57
MRPL10
GJD3
KRT222
KRT40
C17orf50
SLFN13
SLC35G3
UNC45B
CD300LG
KIF18B
RUNDC1
C17orf69
LOC147093
WIPF2
KRT25
TMEM99
SLFN5
NAGS
FAM134C
IMP5
KRT28
KRT24
ARHGAP27
ZNF385C
RDM1
GAS2L2
STH
C17orf66
KIAA1267
C17orf105
FAM171A2
C17orf104
PIGW
C17orf78
LOC284100
CISD3
GSDMA
KRT42P
PTRF
KLHL10
C17orf65
MSL1
KRT27
SLFN14
FLJ43826
STAC2
CCL14-CCL15
KRT26
CCL4L2
C17orf98
LOC388387
CCDC103
RPRML
ARL5C
KRT39
C17orf102
MGC57346
MIR152
TBC1D3B
TBC1D3C
CCL3L3
LOC440434
GPR179
LRRC37A2
FBXO47
SNORA21
LOC644172
LOC644246
KRTAP4-11
MRPL45P2
TBC1D3G
SNORD7
KRTAP4-8
KRTAP2-2
KRTAP9-1
NSFP1
TBC1D3
TBC1D3H
LOC730755
SNORD124
LOC100128977
LOC100130148
LOC100130581
LOC100131347
KRTAP4-9
KRTAP4-7
LOC100133991
C17orf96
LOC100190938
MIR1203
MIR2117
MIR4315-2
MIR2909
MIR4315-1
LOC100505576
LRRC3C
KRTAP16-1
LOC100505782
ARL17B
SLFN12L
RAD51L3-RFFL
MIR4728
MIR4726
MIR4734
MIR4727

Genes in Wide Peak

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

Table S85. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
CLTCL1
hsa-mir-130b
hsa-mir-649
hsa-mir-1286
hsa-mir-1306
hsa-mir-185
hsa-mir-648
hsa-mir-3198
ARVCF
ATP6V1E1
BID
COMT
CRKL
GGT3P
GP1BB
GSC2
SERPIND1
PI4KA
SEPT5
PRODH
RANBP1
SLC7A4
SLC25A1
TBX1
CLDN5
HIRA
UBE2L3
UFD1L
ZNF74
DGCR6
LZTR1
DGCR14
CDC45
P2RX6
SNAP29
DGCR2
TXNRD2
USP18
HIC2
TSSK2
SDF2L1
PPIL2
IL17RA
ANKRD62P1-PARP4P3
POTEH
BCL2L13
DGCR11
DGCR9
DGCR5
DGCR10
TRMT2A
HSFY1P1
CECR6
CECR5
CECR3
CECR2
POM121L8P
YPEL1
ZDHHC8
MED15
TUBA8
CECR1
DGCR8
GNB1L
PEX26
MICAL3
MRPL40
RTN4R
C22orf29
THAP7
OR11H1
SLC25A18
TMEM191A
KLHL22
DGCR6L
RIMBP3
SCARF2
MGC16703
GAB4
C22orf39
C22orf25
CCT8L2
XKR3
LOC150185
LOC150197
AIFM3
RIMBP3C
YDJC
CCDC116
POM121L4P
LOC284865
PI4KAP2
TPTEP1
LOC388849
LOC400891
BCRP2
MIR130B
MIR185
THAP7-AS1
P2RX6P
RIMBP3B
TMEM191C
MIR648
TMEM191B
PI4KAP1
LOC729444
MIR301B
CECR7
CECR5-AS1
FLJ41941
MIR1286
MIR1306
MIR3198-1
MIR3618
SEPT5-GP1BB
MIR4761

Genes in Wide Peak

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

Table S86. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ULK2
AKAP10
SPECC1

Arm-level results

Table 3. Get Full Table Arm-level significance table - 23 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.05 | -0.853 | 1 | 0.03 | -2.22 | 1
1q | 1955 | 0.32 | 21.9 | 0 | 0.04 | -1.57 | 1
2p | 924 | 0.14 | 4.51 | 1.81e-05 | 0.02 | -4.27 | 1
2q | 1556 | 0.09 | 1.35 | 0.345 | 0.02 | -3.61 | 1
3p | 1062 | 0.07 | -0.277 | 1 | 0.08 | -0.102 | 0.959
3q | 1139 | 0.14 | 4.99 | 2.01e-06 | 0.04 | -2.74 | 1
4p | 489 | 0.02 | -4.62 | 1 | 0.12 | 2.82 | 0.0077
4q | 1049 | 0.01 | -5.05 | 1 | 0.11 | 2.62 | 0.0131
5p | 270 | 0.08 | -0.545 | 1 | 0.08 | -0.708 | 1
5q | 1427 | 0.02 | -3.67 | 1 | 0.10 | 1.94 | 0.068
6p | 1173 | 0.08 | 0.672 | 0.815 | 0.02 | -3.92 | 1
6q | 839 | 0.06 | -1.14 | 1 | 0.03 | -3.87 | 1
7p | 641 | 0.08 | 0.0968 | 1 | 0.09 | 0.599 | 0.564
7q | 1277 | 0.09 | 0.925 | 0.629 | 0.08 | 0.213 | 0.786
8p | 580 | 0.18 | 6.65 | 1.18e-10 | 0.17 | 5.82 | 1.62e-08
8q | 859 | 0.24 | 12.2 | 0 | 0.04 | -2.47 | 1
9p | 422 | 0.03 | -4.09 | 1 | 0.17 | 6.26 | 1.29e-09
9q | 1113 | 0.00 | -5.11 | 1 | 0.20 | 9.44 | 0
10p | 409 | 0.20 | 8.2 | 1.08e-15 | 0.07 | -0.946 | 1
10q | 1268 | 0.18 | 8.45 | 0 | 0.07 | -0.41 | 1
11p | 862 | 0.02 | -4.38 | 1 | 0.12 | 2.97 | 0.0052
11q | 1515 | 0.03 | -3.14 | 1 | 0.11 | 3.25 | 0.00227
12p | 575 | 0.08 | -0.214 | 1 | 0.05 | -2.38 | 1
12q | 1447 | 0.06 | -0.801 | 1 | 0.04 | -2.43 | 1
13q | 654 | 0.05 | -1.98 | 1 | 0.11 | 2.05 | 0.0568
14q | 1341 | 0.03 | -3.02 | 1 | 0.08 | 0.75 | 0.491
15q | 1355 | 0.02 | -3.88 | 1 | 0.16 | 6.9 | 2.62e-11
16p | 872 | 0.03 | -3.53 | 1 | 0.14 | 4.51 | 1.41e-05
16q | 702 | 0.01 | -4.48 | 1 | 0.22 | 10.2 | 0
17p | 683 | 0.03 | -3.81 | 1 | 0.20 | 8.46 | 0
17q | 1592 | 0.04 | -1.95 | 1 | 0.14 | 5.4 | 1.61e-07
18p | 143 | 0.07 | -1.7 | 1 | 0.08 | -0.572 | 1
18q | 446 | 0.04 | -3.12 | 1 | 0.10 | 0.998 | 0.388
19p | 995 | 0.07 | -0.279 | 1 | 0.09 | 0.759 | 0.491
19q | 1709 | 0.06 | -0.552 | 1 | 0.07 | 0.194 | 0.786
20p | 355 | 0.11 | 1.68 | 0.201 | 0.03 | -4.04 | 1
20q | 753 | 0.13 | 3.88 | 0.000258 | 0.02 | -4.59 | 1
21q | 509 | 0.04 | -3.08 | 1 | 0.06 | -1.92 | 1
22q | 921 | 0.02 | -3.96 | 1 | 0.17 | 6.7 | 8.12e-11

Methods & Data
Input

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/UCEC/1270164/2.GDAC_MergeDataFiles.Finished/UCEC.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

- Markers File = /xchip/tcga/CancerGenomeAnalysisData/trunk/copynumber/SNP6_annotations/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt

- Reference Genome = /xchip/gistic/variables/hg19/hg19_with_miR_20120227.mat

- CNV Files = /xchip/gistic/CNV/blood_normals/CNV.hg19_111204/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 428 Input Tumor Samples.

Tumor Sample Names
TCGA-A5-A0G1-01A-11D-A120-01
TCGA-A5-A0G2-01A-11D-A042-01
TCGA-A5-A0G5-01A-11D-A042-01
TCGA-A5-A0G9-01A-11D-A042-01
TCGA-A5-A0GA-01A-11D-A042-01
TCGA-A5-A0GB-01A-11D-A042-01
TCGA-A5-A0GD-01A-11D-A042-01
TCGA-A5-A0GE-01A-11D-A042-01
TCGA-A5-A0GG-01A-11D-A120-01
TCGA-A5-A0GH-01A-21D-A042-01

Figure 3. Segmented copy number profiles in the input data

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
Meta

- Maintainer = Dan DiCara

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