Prostate Adenocarcinoma: 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 2.0.16a (cga svn revision 43808).

Summary

There were 152 tumor samples used in this analysis: 18 significant arm-level results, 15 significant focal amplifications, and 29 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 - 15 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
--- | --- | --- | --- | ---
Xq27.1 | 1.5865e-19 | 2.1256e-19 | chrX:138564705-138580758 | 0 [F9]
Xq21.1 | 4.0408e-11 | 2.976e-08 | chrX:79251708-79255479 | 0 [TBX22]
Xq25 | 1.0162e-07 | 6.6622e-06 | chrX:126306276-126315813 | 0 [CXorf64]
Xp22.11 | 0.0002896 | 0.00031043 | chrX:23975644-23983593 | 0 [CXorf58]
Xp22.11 | 0.0002896 | 0.00032881 | chrX:24515774-24522924 | 1
Xq21.1 | 0.00037688 | 0.00037688 | chrX:80829747-80833679 | 0 [SH3BGRL]
3q26.2 | 0.021746 | 0.021746 | chr3:169376291-170116437 | 14
Xp21.1 | 0.044166 | 0.044166 | chrX:35658501-35660210 | 0 [MAGEB16]
Xq25 | 0.037173 | 0.052444 | chrX:122399494-122410812 | 1
Xq21.31 | 0.0093932 | 0.14171 | chrX:87704771-87710744 | 0 [CPXCR1]
8p11.22 | 0.18388 | 0.18388 | chr8:39051902-39137830 | 1
1q21.3 | 0.24405 | 0.24405 | chr1:117180203-162514804 | 492
7p15.3 | 0.24405 | 0.24405 | chr7:17059175-38453654 | 154
12q24.32 | 0.24405 | 0.24405 | chr12:125570198-128729242 | 8
14q21.1 | 0.24405 | 0.24405 | chr14:38008682-38049106 | 1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for Xp22.11.

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

Genes
PDK3

Genes in Wide Peak

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

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

Genes
MECOM
PRKCI
SKIL
TERC
SEC62
GPR160
MYNN
LRRC31
PHC3
ARPM1
LRRC34
LRRIQ4
SAMD7
LOC100128164

Genes in Wide Peak

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

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

Genes
GRIA3

Genes in Wide Peak

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

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

Genes
ADAM32

Genes in Wide Peak

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

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

Genes
ARNT
BCL9
FCGR2B
MUC1
NOTCH2
NTRK1
PRCC
SDHC
TPM3
PDE4DIP
hsa-mir-556
hsa-mir-4259
hsa-mir-765
hsa-mir-9-1
hsa-mir-555
hsa-mir-92b
hsa-mir-4258
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
hsa-mir-942
hsa-mir-320b-1
ADAR
APCS
APOA2
ATP1A2
ATP1A4
BGLAP
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD2
CD5L
CD48
CHRNB2
CKS1B
CLK2
COPA
CRABP2
CRP
CTSK
CTSS
ECM1
EFNA1
EFNA3
EFNA4
ENSA
ETV3
FCER1A
FCER1G
FCGR1A
FCGR1B
FCGR2A
FCGR3A
FCGR3B
FDPS
FLG
FMO5
DARC
GBA
GBAP1
GJA5
GJA8
HDGF
HMGCS2
HSD3B1
HSD3B2
HSPA6
HSPA7
IGSF3
IFI16
IL6R
ILF2
INSRR
IVL
KCNJ9
KCNJ10
KCNN3
LMNA
LOR
LY9
MCL1
SMCP
MEF2D
MNDA
MPZ
MTX1
NDUFS2
NHLH1
NIT1
NPR1
PDZK1
PFDN2
PI4KB
PKLR
PPOX
PRKAB2
PSMB4
PSMD4
PTGFRN
PEX19
RAB13
RFX5
RIT1
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SLAMF1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
SPTA1
SSR2
TBX15
VPS72
THBS3
TCHH
CCT3
TUFT1
USF1
DAP3
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
TAGLN2
ANXA9
TTF2
ITGA10
PEA15
B4GALT3
ADAM15
PEX11B
CD84
SELENBP1
SH2D2A
FCGR2C
PRPF3
ARHGEF2
DEDD
CD101
AIM2
ADAMTS4
SEC22B
CHD1L
SLC25A44
NOS1AP
ARHGEF11
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
NR1I3
SCAMP3
SF3B4
WARS2
PIAS3
HAX1
C1orf61
SEMA6C
POLR3C
TXNIP
PMVK
FAM189B
NES
WDR3
JTB
MTMR11
MAN1A2
MLLT11
SLC27A3
TDRKH
ADAM30
CD160
CELF3
PMF1
DUSP12
VPS45
KIAA0907
ATF6
POGZ
SYT11
RPRD2
SMG5
NCSTN
SNAPIN
RUSC1
CA14
CCDC19
NBPF14
OLFML2B
C1orf43
CHTOP
PHGDH
LCE2B
OR10J1
USP21
SLC39A1
RNF115
LAMTOR2
TMOD4
CERS2
CRNN
DCAF8
F11R
BOLA1
ZBTB7B
RRNAD1
APH1A
PLEKHO1
HAO2
ACP6
GPR89B
UFC1
OAZ3
CD244
DPM3
MRPS21
ADAMTSL4
CRCT1
GDAP2
FAM46C
GON4L
GPATCH4
DUSP23
C1orf56
MSTO1
GOLPH3L
KIRREL
YY1AP1
UBE2Q1
ITLN1
FAM63A
ASH1L
LENEP
SLC50A1
SLAMF8
CDC42SE1
UBQLN4
OTUD7B
RAB25
PGLYRP4
RHBG
ATP8B2
VANGL2
FAM91A2
PBXIP1
S100A14
GATAD2B
CGN
IGSF9
ZNF687
HCN3
SLAMF7
CADM3
PRUNE
HAPLN2
BCAN
SEMA4A
MRPL9
INTS3
SCNM1
FCRL2
MRPL24
TNFAIP8L2
C1orf54
VTCN1
PAQR6
TRIM46
TARS2
TRIM45
FLAD1
OR6N2
OR6K2
PVRL4
SNX27
ANP32E
ISG20L2
FCRL5
FCRL4
REG4
HORMAD1
TOMM40L
POLR3GL
TMEM79
LCE3D
FCRLA
AQP10
SLAMF9
PYGO2
ZNF697
NUP210L
MEX3A
PIGM
IGSF8
C1orf85
PGLYRP3
GNRHR2
SLAMF6
FCRL1
FCRL3
THEM4
SH2D1B
GABPB2
TCHHL1
RPTN
TDRD10
SHE
KLHDC9
HIST2H3C
OR10J5
DCST2
UHMK1
FCRLB
LIX1L
HSD3BP4
C1orf182
IQGAP3
APOA1BP
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
S100A16
ITLN2
CREB3L4
C1orf51
HFE2
ANKRD35
LELP1
DCST1
BNIPL
LRRC71
PYHIN1
SPRR4
PPIAL4A
TTC24
PDIA3P
LCE4A
NBPF11
NUDT17
SPAG17
KRTCAP2
CRTC2
LCE5A
ARHGAP30
C1orf192
RIIAD1
THEM5
NBPF15
ANKRD34A
RUSC1-AS1
C1orf204
C1orf111
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
RXFP4
OR10R2
FCRL6
NBPF7
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
CYCSP52
LOC375010
PEAR1
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
NBPF9
MIR9-1
HIST2H2BF
ETV3L
OR10J3
KPRP
LCE6A
SUMO1P3
HIST2H4B
PRR9
RPL31P11
LOC644242
PPIAL4G
PPIAL4D
LOC645166
LOC645676
POU5F1P4
S100A7L2
LOC646268
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
PCP4L1
SCARNA4
SNORA42
MIR554
MIR555
MIR556
MIR92B
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
MIR765
MIR942
MIR190B
C1orf68
MSTO2P
LOC100130000
TSTD1
LOC100131825
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
LOC100289211
MIR320B1
MIR4257
MIR4258
LOC100505633
LOC100505666
PMF1-BGLAP
TNFAIP8L2-SCNM1
MIR4654

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p15.3.

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

Genes
HNRNPA2B1
HOXA9
HOXA11
HOXA13
JAZF1
hsa-mir-1200
hsa-mir-548n
hsa-mir-550-2
hsa-mir-550-1
hsa-mir-196b
hsa-mir-148a
hsa-mir-1183
hsa-mir-3146
hsa-mir-1302-6
ADCYAP1R1
AHR
AMPH
AOAH
AQP1
SEPT7
CHN2
CLK2P
CRHR2
DFNA5
EVX1
GARS
GHRHR
HOXA1
HOXA2
HOXA3
HOXA4
HOXA5
HOXA6
HOXA7
HOXA10
IL6
ITGB8
NPY
PDE1C
RP9
SFRP4
SP4
TWIST1
DNAH11
TAX1BP1
SKAP2
CREB5
NFE2L3
HDAC9
RAPGEF5
SCRN1
KIAA0087
ELMO1
TRIL
NOD1
GPNMB
IGF2BP3
PPP1R17
NUPL2
HIBADH
INMT
FKBP9
CBX3
AVL9
SNX13
DPY19L1
KIAA0895
LSM5
KBTBD2
OSBPL3
BBS9
SNX10
TRA2A
NT5C3
TXNDC3
MPP6
CYCS
ANLN
CPVL
TOMM7
EPDR1
FKBP14
CDCA7L
KLHL7
STK31
TBX20
NEUROD6
NPVF
HERPUD2
GGCT
EEPD1
STARD3NL
FAM188B
FAM126A
PLEKHA8
CCDC126
C7orf30
C7orf31
BMPER
PRPS1L1
TWISTNB
SP8
HOXA11-AS1
DKFZP586I1420
C7orf41
PRR15
FERD3L
RPL23P8
CCDC129
ZNRF2
TMEM196
STEAP1B
RPS2P32
C7orf71
ABCB5
C7orf46
MACC1
GPR141
NPSR1
LOC401320
LOC401321
LOC401324
AAA1
MIR148A
LOC441204
ZNRF2P1
RP9P
DPY19L2P3
MIR196B
TARP
DPY19L2P1
WIPF3
LOC646762
SNORD93
MIR550A1
MIR550A2
JAZF1-AS1
DPY19L1P1
LOC100130673
LOC100133311
ZNRF2P2
MIR1200
HOTTIP
MIR3146
MIR550B2
MIR550B1
LOC100506178
HOTAIRM1
LOC100506497
LOC100506776
INMT-FAM188B
HOXA10-HOXA9
MIR550A3
KLHL7-AS1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q24.32.

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

Genes
AACS
TMEM132B
LOC387895
LOC400084
FLJ37505
LOC440117
LOC100128554
LOC100507206

Genes in Wide Peak

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

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

Genes
MIPOL1

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 - 29 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
--- | --- | --- | --- | ---
10q23.31 | 1.0164e-40 | 1.0164e-40 | chr10:89617158-90348818 | 3
21q22.3 | 1.264e-27 | 1.264e-27 | chr21:42827479-43100702 | 1
13q14.13 | 3.1123e-25 | 3.1123e-25 | chr13:44358188-48879660 | 31
6q15 | 7.0913e-17 | 7.0913e-17 | chr6:84936364-96030383 | 41
8p21.3 | 6.7657e-15 | 4.0685e-12 | chr8:19532201-27169834 | 69
16q23.3 | 4.1182e-14 | 5.1933e-10 | chr16:84175771-86613674 | 32
12p13.2 | 4.8956e-08 | 4.8221e-08 | chr12:11477536-13523791 | 31
3p13 | 8.881e-08 | 8.881e-08 | chr3:71832385-72941288 | 3
17q21.31 | 1.8607e-07 | 1.8607e-07 | chr17:41831064-42651945 | 28
5q11.2 | 2.6627e-08 | 2.4868e-06 | chr5:54597198-57879426 | 15
5q15 | 1.6415e-08 | 6.6949e-06 | chr5:96515472-101571689 | 8
17p13.1 | 1.1315e-05 | 1.1981e-05 | chr17:6932141-7839690 | 66
11q23.2 | 3.5986e-05 | 3.3051e-05 | chr11:113574880-115045236 | 13
1p31.3 | 2.3909e-05 | 9.5555e-05 | chr1:64643278-66261758 | 12
2q22.1 | 1.4251e-05 | 0.0003093 | chr2:122398475-152105710 | 105
8p11.21 | 1.1417e-06 | 0.012677 | chr8:38850253-42552632 | 28
4q28.1 | 0.037698 | 0.038439 | chr4:118006490-134070791 | 53
18q22.1 | 0.015605 | 0.052426 | chr18:51876581-78077248 | 102
7q36.1 | 0.084854 | 0.081674 | chr7:151211607-152457802 | 8
1q42.2 | 0.12702 | 0.13146 | chr1:211306170-241859551 | 213
16q22.2 | 1.1981e-05 | 0.15457 | chr16:69497204-90354753 | 209
5q22.3 | 0.0027656 | 0.19471 | chr5:111748057-121188594 | 35
1p13.3 | 0.0082566 | 0.20134 | chr1:70666123-149881397 | 420
2q31.1 | 0.0047588 | 0.20134 | chr2:142885913-187459682 | 201
1q23.1 | 0.21575 | 0.21615 | chr1:155269897-196195419 | 406
12q24.33 | 0.21844 | 0.21615 | chr12:103307836-133851895 | 296
3q29 | 0.23327 | 0.23173 | chr3:175078481-198022430 | 186
9p23 | 0.22633 | 0.23173 | chr9:1-25677256 | 113
18q23 | 0.004552 | 0.82355 | chr18:1-78077248 | 342

Genes in Wide Peak

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

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

Genes
PTEN
RNLS
KLLN

Genes in Wide Peak

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

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

Genes
TMPRSS2

Genes in Wide Peak

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

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

Genes
LCP1
CPB2
ESD
GTF2F2
HTR2A
TPT1
SUCLA2
TSC22D1
ITM2B
ZC3H13
LRCH1
NUFIP1
MED4
NUDT15
KIAA1704
KIAA0226L
COG3
LINC00284
LACC1
LINC00330
CCDC122
FAM194B
SPERT
SLC25A30
SIAH3
KCTD4
SERP2
TSC22D1-AS1
SNORA31
TPT1-AS1
LOC100509894

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q15.

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

Genes
CGA
CNR1
EPHA7
GABRR1
GABRR2
HTR1E
NT5E
MAP3K7
RNGTT
TBX18
CASP8AP2
SYNCRIP
SLC35A1
PNRC1
ANKRD6
ZNF292
MDN1
ORC3
SNORD50A
UBE2J1
AKIRIN2
AKIRIN2-AS1
RARS2
C6orf162
LYRM2
SNX14
RRAGD
BACH2
C6orf164
SPACA1
GJA10
PM20D2
SRSF12
C6orf165
C6orf163
GJB7
SNHG5
TSG1
SNORD50B
MIR4464
MIR4643

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p21.3.

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

Genes
hsa-mir-548h-4
hsa-mir-320a
ADRA1A
ATP6V1B2
BMP1
POLR3D
BNIP3L
DPYSL2
EGR3
EPB49
GFRA2
GNRH1
LOXL2
LPL
NEFM
NEFL
NKX3-1
PPP2R2A
PPP3CC
SFTPC
SLC18A1
STC1
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
FGF17
DOK2
ENTPD4
PHYHIP
SORBS3
NPM2
PNMA2
ADAM28
LZTS1
XPO7
TRIM35
RHOBTB2
SLC39A14
ADAMDEC1
SLC25A37
KCTD9
PIWIL2
INTS10
HR
BIN3
KIAA1967
PDLIM2
EBF2
FAM160B2
NUDT18
DOCK5
FLJ14107
REEP4
STMN4
CHMP7
NKX2-6
PEBP4
CDCA2
R3HCC1
LGI3
LOC254896
LOC286059
LOC286114
LOC389641
MIR320A
C8orf58
LOC100507156

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q23.3.

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

Genes
hsa-mir-1910
COX4I1
FOXF1
FOXC2
IRF8
TAF1C
USP10
KIAA0513
ATP2C2
COX4NB
KIAA0182
COTL1
GINS2
ZDHHC7
KIAA1609
WFDC1
MTHFSD
KLHL36
CRISPLD2
KCNG4
DNAAF1
FLJ30679
LOC146513
ADAD2
LINC00311
FAM92B
LOC400548
LOC400550
C16orf74
LOC727710
LOC732275
MIR1910

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.2.

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

Genes
ETV6
hsa-mir-614
hsa-mir-613
CDKN1B
CREBL2
EMP1
GPR19
LRP6
PRB1
GPRC5A
HEBP1
DDX47
MANSC1
GPRC5D
KIAA1467
BCL2L14
DUSP16
APOLD1
GSG1
HTR7P1
LOH12CR1
LOC338817
RPL13AP20
LOH12CR2
PRB2
MIR613
MIR614
MIR1244-1
MIR1244-3
MIR1244-2
LOC100506314

Genes in Wide Peak

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

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

Genes
RYBP
SHQ1
LOC201617

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q21.31.

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

Genes
DUSP3
FZD2
GRN
ITGA2B
MPP2
MPP3
PPY
PYY
SLC4A1
UBTF
HDAC5
RUNDC3A
GPATCH8
FAM215A
SOST
SLC25A39
ATXN7L3
C17orf53
TMUB2
TMEM101
G6PC3
ASB16
LSM12
CD300LG
NAGS
C17orf105
FAM171A2
C17orf65

Genes in Wide Peak

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

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

Genes
IL6ST
MAP3K1
PPAP2A
PLK2
SKIV2L2
DDX4
GPBP1
ANKRD55
C5orf35
IL31RA
SLC38A9
MIER3
GAPT
ACTBL2
RNF138P1

Genes in Wide Peak

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

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

Genes
hsa-mir-548p
CHD1
ST8SIA4
RGMB
FAM174A
FLJ35946
LOC100133050
LOC100289230

Genes in Wide Peak

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

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

Genes
TP53
hsa-mir-324
ACADVL
ASGR1
ASGR2
ATP1B2
CD68
CHD3
CHRNB1
CLDN7
DLG4
DVL2
EFNB3
EIF4A1
EIF5A
FGF11
GPS2
POLR2A
SHBG
SLC2A4
SOX15
TNK1
TNFSF13
TNFSF12
KCNAB3
FXR2
MPDU1
ACAP1
CLEC10A
GABARAP
KDM6B
CTDNEP1
C17orf81
SENP3
SNORA67
YBX2
WRAP53
PLSCR3
NLGN2
ZBTB4
TRAPPC1
PHF23
LSMD1
NEURL4
TMEM88
SAT2
RPL29P2
CYB5D1
DNAH2
KCTD11
SLC16A11
SLC16A13
C17orf74
C17orf61
LOC284023
TMEM102
TMEM95
SPEM1
TNFSF12-TNFSF13
MIR324
SLC35G6
SNORA48
SNORD10
SCARNA21
C17orf61-PLSCR3
SENP3-EIF4A1

Genes in Wide Peak

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

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

Genes
HTR3A
NNMT
ZBTB16
HTR3B
ZW10
RBM7
REXO2
C11orf71
FAM55D
USP28
FAM55A
FAM55B
CLDN25

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p31.3.

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

Genes
JAK1
hsa-mir-101-1
AK4
LEPR
DNAJC6
LEPROT
RAVER2
CACHD1
UBE2U
MIR101-1
MIR3671
MIR4794

Genes in Wide Peak

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

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

Genes
ERCC3
hsa-mir-128-1
hsa-mir-663b
ACVR2A
BIN1
RND3
CCNT2
DARS
GPR17
GPR39
GYPC
HNMT
KIF5C
LCT
MCM6
MGAT5
MYO7B
ORC4
POLR2D
PROC
TSN
CXCR4
KYNU
HS6ST1
ZEB2
MAP3K2
NXPH2
RAB3GAP1
UBXN4
R3HDM1
EPC2
PTPN18
MMADHC
C2orf27A
ARHGEF4
LRP1B
PLEKHB2
WDR33
SMPD4
IWS1
LIMS2
MBD5
ARHGAP15
CFC1
UGGT1
SAP130
GTDC1
MZT2B
YSK4
THSD7B
TMEM163
AMMECR1L
ZRANB3
RAB6C
CCDC115
MKI67IP
SFT2D3
CCDC74A
CCDC74B
IMP4
TUBA3E
TUBA3D
LYPD1
CNTNAP5
ACMSD
FAM168B
LYPD6
LYPD6B
LOC150527
LOC150776
WTH3DI
FAM123C
LOC254128
LOC285103
SPOPL
CYP27C1
NCKAP5
GPR148
LOC389033
LOC389043
LOC401010
DKFZp686O1327
MIR128-1
C2orf27B
LOC440905
LOC440910
POTEKP
POTEE
ANKRD30BL
LOC646743
LOC647012
CFC1B
MZT2A
POTEF
PABPC1P2
LOC100129961
LOC100131320
CYP4F30P
LOC100216479
ZEB2-AS1
MIR663B
MIR3679
LOC100507600
MIR4783
MIR4784

Genes in Wide Peak

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

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

Genes
hsa-mir-486
ANK1
ADAM3A
ADAM2
IKBKB
IDO1
PLAT
POLB
SFRP1
SLC20A2
VDAC3
KAT6A
ADAM18
ADAM9
AP3M2
DKK4
GOLGA7
C8orf4
ZMAT4
GINS4
C8orf40
AGPAT6
NKX6-3
IDO2
ADAM32
ADAM5P
MIR486
LOC100130964

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q28.1.

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

Genes
IL2
hsa-mir-2054
ANXA5
CCNA2
FABP2
FGF2
MAD2L1
EXOSC9
TRPC3
PRSS12
PDE5A
NDST3
SEC24D
SPRY1
PGRMC2
PLK4
PRDM5
NUDT6
HSPA4L
INTU
MYOZ2
USP53
LARP1B
BBS7
ANKRD50
METTL14
IL21
NDNF
FAT4
TNIP3
PHF17
C4orf29
SLC25A31
QRFPR
KIAA1109
SCLT1
C4orf33
TMEM155
ADAD1
SPATA5
BBS12
SYNPO2
MFSD8
LOC285419
FLJ14186
C4orf3
CEP170P1
LOC645513
SNORA24
CETN4P
SNHG8
PP12613
MIR2054

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q22.1.

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

Genes
BCL2
MALT1
hsa-mir-122
CDH7
CYB5A
FECH
KDSR
GALR1
GRP
LMAN1
MBP
MC4R
NARS
NFATC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PMAIP1
RAB27B
SERPINB3
SERPINB4
TCF4
ZNF236
SERPINB7
TNFRSF11A
CTDP1
SOCS6
TXNL1
ONECUT2
VPS4B
ZNF516
TSHZ1
CD226
TXNL4A
ADNP2
PHLPP1
NEDD4L
WDR7
PIGN
RTTN
KCNG2
SALL3
CDH20
CDH19
TIMM21
RAX
ST8SIA3
TMX3
ZCCHC2
ZNF532
ZNF407
CNDP2
KIAA1468
CCDC102B
RBFA
PQLC1
CCDC68
NETO1
PARD6G
CNDP1
SERPINB12
SERPINB11
SEC11C
DSEL
ALPK2
FAM69C
CCBE1
CBLN2
C18orf54
FBXO15
DOK6
RNF152
LINC00305
C18orf26
BOD1P
ZADH2
C18orf62
LOC284276
HMSD
LOC284294
LOC339298
CPLX4
ATP9B
LOC390858
LOC400654
LOC400655
LOC400657
MIR122
HSBP1L1
LOC643542
C18orf63
LOC100130522
LOC100131655
LOC100505474
LOC100505549
LOC100505776
LOC100505817
MIR4529
MIR3591

Genes in Wide Peak

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

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

Genes
MLL3
XRCC2
PRKAG2
GALNT11
GALNTL5
FABP5P3
LOC100128822
LOC100505483

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1q42.2.

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

Genes
FH
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
ACTA1
ACTN2
PARP1
AGT
ARF1
ATF3
CAPN2
CENPF
CHML
LYST
CHRM3
EPHX1
EPRS
ESRRG
GALNT2
GNG4
GUK1
H3F3A
HLX
ITPKB
KCNK1
KCNK2
LBR
LGALS8
MARK1
MTR
NEK2
NID1
NVL
PPP2R5A
PROX1
PSEN2
PTPN14
RAB4A
RGS7
RYR2
SRP9
AURKAPS1
TARBP1
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TP53BP2
TRAF5
TSNAX
USH2A
WNT9A
SLC30A1
HIST3H3
GNPAT
CDC42BPA
DEGS1
KMO
TAF1A
GGPS1
TMEM63A
TOMM20
URB2
LPGAT1
BPNT1
LEFTY1
SPHAR
CAPN9
DUSP10
COG2
RBM34
FBXO28
ABCB10
OPN3
RAB3GAP2
INTS7
NSL1
RPS6KC1
RNU5F-1
TAF5L
DISC2
DISC1
FLVCR1
CNIH4
PYCR2
NENF
RRP15
TRIM17
KCTD3
DTL
ARID4B
EGLN1
KIAA1383
MARC2
SUSD4
GPATCH2
HEATR1
TMEM206
BATF3
SLC30A10
IARS2
ENAH
NUP133
RCOR3
ERO1LB
FMN2
SMYD2
ADCK3
GJC2
SIPA1L2
ZP4
RHOU
GREM2
ACBD3
MARC1
ARV1
AIDA
JMJD4
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
VASH2
PCNXL2
WDR26
TRIM11
MIXL1
C1orf124
OBSCN
NTPCR
KIAA1804
LINC00467
C1orf198
DISP1
WNT3A
ANGEL2
HIST3H2A
SNAP47
C1orf96
LYPLAL1
DNAH14
C1orf131
SPATA17
EDARADD
MRPL55
HIST3H2BB
TATDN3
BROX
SLC35F3
B3GALNT2
CNIH3
EXOC8
RNF187
C1orf227
FAM71A
C1orf55
C1orf65
IBA57
LIN9
ZNF678
PRSS38
LOC339535
RD3
IRF2BP2
MIA3
C1orf95
FAM89A
CAPN8
C1orf31
C1orf140
FAM177B
ZNF847P
MIR194-1
MIR215
TRIM67
H3F3AP4
DUSP5P
FLVCR1-AS1
LOC643723
SNRPD2P2
RPS7P5
SNORA14B
SNORA36B
SNORA16B
LOC728463
LOC100130093
LOC100130331
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
MIR664
LINC00184
TSNAX-DISC1
MIR320B2
MIR3123
MIR3122
MIR3620
PROX1-AS1
LOC100506795
LOC100506810
MIR4753
MIR4666A
MIR4671
MIR4427
MIR4742
LINC00538

Genes in Wide Peak

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

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

Genes
CBFA2T3
FANCA
MAF
hsa-mir-1910
hsa-mir-3182
hsa-mir-1972-2
hsa-mir-140
hsa-mir-1538
AARS
AP1G1
AFG3L1P
APRT
ZFHX3
C16orf3
CA5A
CALB2
CDH13
CDH15
COX4I1
CTRB1
CYBA
DHODH
NQO1
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GLG1
HP
HPR
HSBP1
HSD17B2
IRF8
KARS
MC1R
CHST6
MVD
CHMP1A
PLCG2
PSMD7
RPL13
ST3GAL2
SPG7
TAT
ZNF19
ZNF23
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
BCAR1
C16orf7
KIAA0513
PIEZO1
DHX38
IST1
ATP2C2
CLEC3A
CHST4
MPHOSPH6
COX4NB
TUBB3
CFDP1
NFAT5
WWP2
PRDM7
DDX19B
GABARAPL2
MON1B
TCF25
PHLPP2
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
SF3B3
ADAT1
CHST5
COG4
CPNE7
IL17C
NOB1
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCMO1
TERF2IP
NECAB2
KLHDC4
HYDIN
DEF8
TXNL4B
BANP
PDPR
RFWD3
DDX19A
ZNF821
ZDHHC7
VAC14
FTSJD1
CENPN
C16orf61
JPH3
VAT1L
KIAA1609
WFDC1
MTHFSD
DBNDD1
FA2H
TMEM231
WDR59
KLHL36
FBXO31
CMIP
CDT1
MAP1LC3B
PMFBP1
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
ZNRF1
CNTNAP4
MARVELD3
MTSS1L
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
EXOSC6
C16orf46
DNAAF1
SPATA2L
C16orf55
ZC3H18
CDYL2
TMEM170A
SLC38A8
SLC22A31
IL34
FLJ30679
LOC146513
ZFPM1
ADAD2
ZFP1
ADAMTS18
MGC23284
LINC00311
LDHD
FUK
MLKL
ZNF778
ACSF3
LINC00304
HTA
LOC283922
NUDT7
PDXDC2P
CLEC18C
SNAI3
FAM92B
ATXN1L
PKD1L3
CLEC18A
CTU2
PABPN1L
LOC400548
LOC400550
LOC400558
C16orf74
MIR140
CTRB2
CLEC18B
SNORD68
SNORD71
SNORD111
LOC727710
LOC729513
LOC732275
SNORD111B
LOC100128881
LOC100129617
LOC100130015
LOC100130894
SYCE1L
LOC100287036
MIR1538
MIR1972-1
MIR1910
SNORA70D
MIR3182
MIR1972-2
LOC100506083
LOC100506172
C16orf95
MIR4720
MIR4722
MIR4719

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q22.3.

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

Genes
APC
hsa-mir-1244-2
CDO1
AP3S1
DMXL1
HSD17B4
KCNN2
MCC
PGGT1B
SRP19
REEP5
ATG12
TNFAIP8
TMED7
PRR16
COMMD10
FLJ11235
TRIM36
FEM1C
SEMA6A
YTHDC2
TSSK1B
FTMT
CCDC112
DCP2
AQPEP
DTWD2
FAM170A
TICAM2
LOC644100
LOC728342
MIR1244-1
TMED7-TICAM2
MIR1244-3
MIR1244-2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p13.3.

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

Genes
BCL9
NOTCH2
NRAS
BCL10
PDE4DIP
TRIM33
RBM15
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
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
ABCA4
ACADM
ADORA3
AGL
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
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
FCGR1A
FCGR1B
FMO5
GBP1
GBP2
GBP3
GFI1
GJA5
GJA8
GCLM
GNAI3
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
HMGCS2
HSD3B1
HSD3B2
IGSF3
CYR61
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
MSH4
NGF
NHLH2
OVGP1
PDZK1
PRKAB2
PRKACB
PKN2
PSMA5
PTGER3
PTGFR
PTGFRN
ABCD3
RABGGTB
RAP1A
SNORD21
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TGFBR3
TSHB
VCAM1
WNT2B
CSDE1
EVI5
CDC7
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
BCAR3
TTF2
ITGA10
LMO4
CDC14A
RTCD1
FPGT
PEX11B
FUBP1
SLC16A4
SRSF11
CD101
SEP15
ZRANB2
ARHGAP29
SEC22B
CHD1L
CLCA3P
CLCA2
HS2ST1
LRIG2
LPPR4
RBM8A
PIGK
TSPAN2
BCAS2
WARS2
CEPT1
PIAS3
VAV3
HBXIP
IFI44
POLR3C
TXNIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
IFI44L
DNAJB4
ADAM30
CD160
GLMN
HHLA3
DDX20
CLCA4
MTF2
NTNG1
WDR47
USP33
CLCC1
LPHN2
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
NBPF14
RWDD3
ZZZ3
PTPN22
PHGDH
AK5
SNORA66
SNORD45B
SNORD45A
CHIA
RNF115
GPSM2
SLC25A24
DNTTIP2
TMED5
BOLA1
TNNI3K
SH3GLB1
HAO2
ACP6
SNX7
GPR89B
DPH5
GPR88
CCDC76
RSBN1
ZNHIT6
GIPC2
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
MCOLN3
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
CCBL2
TMEM167B
OLFML3
FAM91A2
AMIGO1
ODF2L
KIAA1324
PTBP2
DNASE2B
ELTD1
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
TTLL7
RPAP2
DENND2D
RPF1
SIKE1
TRIM45
ANKRD13C
VANGL1
ST6GALNAC5
GPR61
REG4
SYDE2
ZNF644
LRRC8C
POLR3GL
PROK1
PSRC1
ATP1A1OS
FAM40A
ZNF697
NEXN
DNAJA1P5
HENMT1
GNRHR2
GBP4
GBP5
SSX2IP
OLFM3
WDR63
MAB21L3
HIST2H3C
SLC44A3
ATXN7L2
C1orf194
ASB17
TYW3
C1orf173
LRRIQ3
LRRC39
LIX1L
HSD3BP4
DRAM2
C1orf88
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
HFE2
ANKRD35
SLC30A7
MGC27382
RP11-165H20.1
DENND2C
GBP6
LPPR5
FNDC7
SASS6
PPIAL4A
HFM1
UBL4B
PDIA3P
ALG14
NBPF11
NUDT17
SPAG17
HIPK1
SLC44A5
AKR7A2P1
EPHX4
AKNAD1
MCOLN2
COL24A1
ST6GALNAC3
NEGR1
MAGI3
FAM19A3
NBPF15
FAM102B
SYPL2
CYB561D1
ANKRD34A
ZNF326
BTBD8
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BC
HIST2H2BA
LOC339524
CCDC18
MYBPHL
BARHL2
HSP90B3P
NBPF7
FAM73A
LOC375010
GBP7
C1orf146
FAM69A
SLC6A17
NOTCH2NL
FLJ39739
LOC388692
UOX
FRRS1
GBP1P1
FLJ27354
MIR137HG
NBPF9
MIR137
MIR186
MIR197
LHX8
C1orf180
FLJ31662
LOC440600
BCL2L15
HIST2H2BF
PGCP1
GEMIN8P4
RBMXL1
HIST2H4B
SRG7
CYMP
LOC643441
LOC644242
PPIAL4G
PPIAL4D
LOC645166
LOC646626
EMBP1
SRGAP2P2
LOC648740
NBPF6
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
SCARNA2
SNORD45C
MIR548D1
MIR553
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
LOC729970
LOC729987
PPIAL4E
PFN1P2
MIR942
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129269
LOC100129620
LOC100130000
LOC100131564
NBPF10
FCGR1C
ZRANB2-AS1
LOC100286793
LOC100287722
LOC100289211
MIR320B1
MIR4256
MIR548AA1
LOC100505768
LOC100506343
FPGT-TNNI3K
TMEM56-RWDD3
MIR2682
MIR4423
NEGR1-IT1
ZRANB2-AS2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2q31.1.

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

Genes
CHN1
HOXD11
HOXD13
NFE2L2
hsa-mir-1258
hsa-mir-3128
hsa-mir-1246
hsa-mir-10b
hsa-mir-933
ACVR1
ACVR2A
RND3
ATP5G3
CACNB4
CHRNA1
ATF2
DLX1
DLX2
DYNC1I2
DPP4
FAP
FRZB
GAD1
GALNT3
GCG
GPD2
GRB14
HOXD1
HOXD3
HOXD4
HOXD8
HOXD9
HOXD10
HOXD12
ITGA6
ITGA4
ITGB6
KCNJ3
KIF5C
LRP2
LY75
NEB
NEUROD1
NR4A2
ORC4
PDE1A
PDK1
RBMS1
SCN1A
SCN2A
SCN3A
SCN7A
SCN9A
SP3
SSB
SSFA2
TNFAIP6
TTN
WIPF1
PKP4
HAT1
AGPS
PRKRA
SLC25A12
ABCB11
B3GALT1
KYNU
NMI
PPIG
CIR1
CYTIP
ZEB2
TLK1
CD302
TANK
DHRS9
PSMD14
STAM2
KBTBD10
UBE2E3
MTX2
TBR1
NCKAP1
RAPGEF4
GALNT5
COBLL1
PLA2R1
GCA
GORASP2
EPC2
ARL5A
MMADHC
STK39
METTL5
OLA1
BAZ2B
PDE11A
FKBP7
ZAK
DNAJC10
FIGN
RIF1
PRPF40A
MBD5
ARHGAP15
ZC3H15
RPRM
SLC4A10
SPC25
ERMN
CWC22
G6PC2
IFIH1
MARCH7
PLEKHA3
SCRN3
FASTKD1
GTDC1
TTC21B
METTL8
CYBRD1
CSRNP3
DCAF17
KIAA1715
CDCA7
TANC1
KCNH7
LOC91149
SESTD1
ZNF804A
TTC30A
DAPL1
FMNL2
GALNT13
OSBPL6
NOSTRIN
NUP35
XIRP2
RBM45
BBS5
C2orf77
ACVR1C
UBR3
LYPD6
LYPD6B
CCDC148
MYO3B
DUSP19
TTC30B
ZNF385B
ARL6IP6
KLHL23
PPP1R1C
SLC38A11
WDSUB1
UPP2
GPR155
HNRNPA3
CERS6
METAP1D
CCDC141
LOC285084
MLK7-AS1
EVX2
RBM43
LOC375295
CERKL
SP5
DKFZp686O1327
LOC401022
FSIP2
MIR10B
LOC440925
PHOSPHO2
DFNB59
LOC554201
PABPC1P2
MIR933
LOC100130691
SP9
LOC100144595
MIR1246
MIR548N
MIR1258
ZEB2-AS1
SNORA70F
MIR3128
LOC100505695
LOC100506124
LOC100506134
LOC100506783
LOC100506866
LY75-CD302
PHOSPHO2-KLHL23
MIR4437
MIR4774
MIR4785
MIR4773-1
MIR4444-1
MIR4773-2
LOC100861402

Genes in Wide Peak

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

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

Genes
ABL2
FCGR2B
NTRK1
PBX1
PRCC
SDHC
TPR
hsa-mir-1278
hsa-mir-3121
hsa-mir-488
hsa-mir-199a-2
hsa-mir-1295
hsa-mir-3119-2
hsa-mir-557
hsa-mir-1255b-2
hsa-mir-921
hsa-mir-556
hsa-mir-4259
hsa-mir-765
hsa-mir-9-1
hsa-mir-555
ALDH9A1
APCS
APOA2
FASLG
ASTN1
SERPINC1
ATP1A2
ATP1A4
ATP1B1
BGLAP
CACNA1E
CASQ1
CD1A
CD1B
CD1C
CD1D
CD1E
CD247
CD5L
CD48
COPA
CRABP2
CRP
DHX9
DPT
ETV3
F5
FCER1A
FCER1G
FCGR2A
FCGR3A
FCGR3B
FDPS
FMO1
FMO2
FMO3
FMO4
DARC
GLUL
HDGF
MR1
HSPA6
HSPA7
IFI16
INSRR
KCNJ9
KCNJ10
LAMC1
LAMC2
LMNA
LMX1A
LY9
MEF2D
MGST3
MNDA
MPZ
MYOC
NCF2
NDUFS2
NHLH1
NIT1
DDR2
PDC
PFDN2
PIGC
PLA2G4A
PRRX1
POU2F1
PPOX
PTGS2
QSOX1
PEX19
RGS1
RGS2
RGS4
RGS13
RGS16
RIT1
RNASEL
RNF2
RXRG
XCL1
SELE
SELL
SELP
SLAMF1
SOAT1
UAP1
SPTA1
TROVE2
SSR2
XCL2
TNR
TOP1P1
CCT3
TNFSF4
UCK2
USF1
DAP3
NPHS2
TAGLN2
RGS5
BLZF1
VAMP4
PEA15
B4GALT3
B3GALT2
CREG1
CD84
TNFSF18
MPZL1
SH2D2A
ANGPTL1
TBX19
FCGR2C
ARHGEF2
DEDD
XPR1
GPR52
AIM2
RASAL2
ADAMTS4
PRDX6
SLC25A44
KIAA0040
NOS1AP
ARHGEF11
CEP350
SMG7
RABGAP1L
FAM20B
NR1I3
ARPC5
PRG4
GPA33
STX6
C1orf61
SLC19A2
IVNS1ABP
NES
OCLM
PMF1
DUSP12
KIAA0907
KIFAP3
ATF6
NMNAT2
GLT25D2
RGL1
SYT11
PRRC2C
SMG5
NCSTN
GPR161
RUSC1
CCDC19
BRP44
OLFML2B
DNM3
TOR1AIP1
OR10J1
SNORD81
SNORD79
SNORD80
SNORD47
SNORD44
USP21
CACYBP
KLHL20
LAMTOR2
NME7
DCAF8
F11R
GLRX2
RRNAD1
IER5
UCHL5
C1orf9
HSD17B7
UFC1
METTL13
CD244
TMCO1
SWT1
GON4L
GPATCH4
DUSP23
C1orf27
RALGPS2
MSTO1
DARS2
KIRREL
YY1AP1
ITLN1
C1orf112
ADCY10
DCAF6
ASH1L
SLAMF8
UBQLN4
RAB25
RHBG
SCYL3
VANGL2
IGSF9
POGK
KIAA1614
FAM5B
C1orf114
SLAMF7
CADM3
HAPLN2
GAS5
PAPPA2
BCAN
TNN
MRPS14
SEMA4A
TOR3A
RFWD2
RGS18
MGC4473
FCRL2
CDC73
MRPL24
PAQR6
C1orf129
EDEM3
NPL
OR6N2
OR6K2
C1orf21
PVRL4
SHCBP1L
TRMT1L
ISG20L2
FCRL5
FCRL4
NUF2
HMCN1
C1orf49
TOMM40L
TMEM79
ACBD6
ZBTB37
FCRLA
ANKRD36BP1
MAEL
RGS8
SEC16B
LHX4
SLAMF9
CENPL
DUSP27
RCSD1
MEX3A
METTL18
GORAB
C1orf105
PIGM
IGSF8
C1orf85
SLAMF6
FCRL1
FCRL3
FMO9P
TSEN15
FAM129A
TADA1
SH2D1B
KLHDC9
AXDND1
OR10J5
ZNF648
TEDDM1
UHMK1
FCRLB
C1orf182
IQGAP3
APOA1BP
OR10T2
OR6P1
OR10X1
OR10Z1
OR6K6
OR6N1
ITLN2
FAM163A
RC3H1
METTL11B
FAM78B
LRRC71
PYHIN1
TDRD5
TOR1AIP2
TTC24
FLJ23867
ARHGAP30
C1orf192
TIPRL
SLC9A11
RUSC1-AS1
LOC284648
DKFZP564C196
C1orf204
C1orf111
LOC284688
RXFP4
ANKRD45
FAM5C
C1orf110
OR10R2
FCRL6
RGSL1
CYCSP52
PEAR1
SFT2D2
ILDR2
FMO6P
LINC00272
VHLL
OR10K2
OR10K1
OR6Y1
OR6K3
VSIG8
C1orf226
LOC400794
C1orf220
APOBEC4
MIR199A2
MIR214
MIR9-1
RGS21
ETV3L
LRRC52
LOC440700
LOC440704
OR10J3
SUMO1P3
MIR488
SNORD74
RPL31P11
LOC645676
POU5F1P4
LOC646268
PCP4L1
SCARNA3
SCARNA4
SNORA42
SNORD75
SNORD76
SNORD77
SNORD78
MIR555
MIR556
MIR557
LOC730102
LOC730159
MIR765
MIR921
MSTO2P
TSTD1
LOC100131825
GM140
LOC100288079
MIR1278
MIR1295A
MIR548F1
LOC100302401
MIR3119-1
MIR3120
MIR3119-2
MIR3121
MIR3658
LOC100505633
LOC100505795
LOC100505918
LOC100506023
LOC100506046
PMF1-BGLAP
LOC100527964
MIR4424
MIR4654
DNM3OS

Genes in Wide Peak

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

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

Genes
ALDH2
BCL7A
PTPN11
hsa-mir-4304
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
hsa-mir-619
ACACB
ACADS
ASCL1
ATP2A2
SCARB1
CMKLR1
COX6A1
CRY1
DAO
DTX1
EIF2B1
STX2
GOLGA3
GTF2H3
HPD
MMP17
MSI1
MVK
MYL2
NFYB
NOS1
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PLA2G1B
POLE
PPP1CC
PRKAB1
PSMD9
PXMP2
PXN
RAN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
TBX5
TBX3
HNF1A
TDG
HSP90B1
TXNRD1
UBC
UNG
ZNF10
ZNF26
ZNF84
ZNF140
CDK2AP1
BRAP
ULK1
RASAL1
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
HRK
ADAM1
HCAR3
HIP1R
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
SH2B3
ARPC3
MPHOSPH9
CAMKK2
ZNF268
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
SDS
RAB35
SNRNP35
PRDM4
CIT
PWP1
FICD
FZD10
MLXIP
RPH3A
P2RX2
FBXO21
SETD1B
ANKLE2
CUX2
KIAA1033
MED13L
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
FBXW8
HSPB8
HCAR1
IFT81
FAM216A
HCFC2
CHST11
GALNT9
GPN3
GLTP
C12orf47
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
RIC8B
APPL2
SBNO1
SVOP
STAB2
ZCCHC8
POLR3B
CHFR
WSB2
DIABLO
PITPNM2
EP400
DHX37
FBRSL1
DDX55
TRPV4
LHX5
SUDS3
C12orf43
VPS33A
RSRC2
AACS
DDX54
NOC4L
B3GNT4
TCTN1
OGFOD2
VPS37B
C12orf49
TCTN2
NAA25
SLC24A6
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
KCTD10
SLC41A2
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
UNC119B
USP30
ORAI1
RNFT2
C12orf34
C12orf52
MGC14436
ANKRD13A
TMEM116
UBE3B
C12orf23
C12orf65
TMEM132C
CCDC64
SDSL
TMEM132B
IQCD
LOC116437
C12orf45
TMEM132D
SLC15A4
ASCL4
BTBD11
ALKBH2
FOXN4
SPPL3
BRI3BP
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
RAD9B
FAM109A
LOC144742
ALDH1L2
PPTC7
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
PLBD2
GNN
LRRC43
TCP11L2
LOC255480
GPR133
MORN3
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
DDX51
MMAB
HCAR2
TMEM119
LOC338799
EP400NL
RILPL1
C12orf42
IL31
C12orf75
CCDC42B
TMEM233
SETD8
LOC387895
C12orf76
LOC400084
FLJ37505
LOC440117
FLJ31485
EID3
MAP1LC3B2
LOC647589
SNORA49
MIR620
C12orf73
LOC728739
LOC100128554
LOC100130238
LOC100131138
LOC100131733
LOC100190940
LINC00173
LOC100287944
ZNF605
MIR1178
MIR4304
MIR3612
MIR3652
MIR3922
MIR3908
LOC100505978
LOC100506649
LOC100506668
LOC100507055
LOC100507066
LOC100507091
LOC100507206
ZNF664-FAM101A
MIR4498
MIR4472-2
MIR4700
MIR4497

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3q29.

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

Genes
BCL6
EIF4A2
ETV5
LPP
PIK3CA
SOX2
TFRC
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
ACTL6A
AHSG
APOD
BDH1
AP2M1
CLCN2
CPN2
CRYGS
DGKG
DLG1
DVL3
EHHADH
EIF4G1
EPHB3
FGF12
GP5
HRG
HES1
IL1RAP
KNG1
MFI2
MUC4
NDUFB5
OPA1
PAK2
PCYT1A
POLR2H
PPP1R2
MASP1
PSMD2
RFC4
SNORA63
RPL35A
TRA2B
ST6GAL1
SST
THPO
FXR1
TP63
CHRD
EIF2B5
USP13
CLDN1
MAP3K13
ADIPOQ
KIAA0226
ECE2
ABCC5
TNK2
ALG3
KCNMB2
IGF2BP2
CLDN16
NCBP2
MCF2L2
ATP11B
VPS8
ACAP2
UBXN7
FETUB
LAMP3
KCNMB3
ZNF639
PEX5L
DNAJB11
DCUN1D1
KLHL24
PIGX
TBCCD1
LEPREL1
ABCF3
LSG1
PARL
MFN1
YEATS2
MCCC1
HRASLS
MRPL47
SENP2
GNB4
RTP4
MAGEF1
ZMAT3
ATP13A3
TBL1XR1
MAP6D1
PIGZ
B3GNT5
IQCG
ATP13A4
FYTTD1
MGC2889
LRCH3
CEP19
LMLN
KLHL6
VWA5B2
TMEM41A
TMEM44
CAMK2N2
TM4SF19
RPL39L
DNAJC19
FAM131A
ZDHHC19
LRRC15
FAM43A
TMEM207
RTP1
TTC14
MB21D2
XXYLT1
CCDC50
PYDC2
LOC152217
RNF168
HTR3C
LIPH
HTR3D
OSTalpha
FBXO45
MUC20
SENP5
LOC220729
LOC253573
TCTEX1D2
C3orf43
SDHAP1
UTS2D
HTR3E
C3orf70
TPRG1
CCDC39
LOC339926
LPP-AS2
LOC344887
RTP2
OSTN
ATP13A5
SOX2-OT
WDR53
ANKRD18DP
LRRC33
FLJ46066
FLJ42393
FLJ34208
LOC401109
SNORD2
SNORA4
C3orf65
GMNC
LOC647323
SNORA81
SNORD66
MIR570
SDHAP2
FAM157A
MIR922
MIR944
LOC100128023
LOC100131551
LOC100131635
SNAR-I
MIR1224
MIR1248
LOC100505687
MFI2-AS1
LOC100507086
LOC100507391
TM4SF19-TCTEX1D2
MIR4797
MIR4789

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p23.

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

Genes
JAK2
MLLT3
NFIB
CD274
hsa-mir-31
hsa-mir-491
hsa-mir-3152
hsa-mir-101-2
hsa-mir-1302-9
PLIN2
CDKN2A
CDKN2B
DMRT1
ELAVL2
FOXD4
MLANA
GLDC
IFNA1
IFNA2
IFNA4
IFNA5
IFNA6
IFNA7
IFNA8
IFNA10
IFNA13
IFNA14
IFNA16
IFNA17
IFNA21
IFNA22P
IFNB1
IFNW1
INSL4
MTAP
PTPRD
RFX3
RLN1
RLN2
RPS6
SH3GL2
SLC1A1
SMARCA2
SNAPC3
TYRP1
VLDLR
MPDZ
CER1
KIAA0020
RCL1
DMRT2
RRAGA
PSIP1
INSL6
KDM4C
KANK1
SLC24A2
RANBP6
AK3
C9orf53
BNC2
HAUS6
CNTLN
KIAA1797
C9orf68
CDC37L1
DENND4C
C9orf46
CBWD1
KLHL9
KIAA1432
DMRT3
DMRTA1
ERMP1
PDCD1LG2
DOCK8
GLIS3-AS1
TPD52L3
IL33
C9orf123
ADAMTSL1
UHRF2
C9orf66
TTC39B
FAM154A
FREM1
KIAA2026
KCNV2
GLIS3
C9orf93
LURAP1L
IFNE
ZDHHC21
ACER2
LOC389705
FLJ35024
FLJ41200
PTPLAD2
PPAPDC2
MIR101-2
MIR31
FLJ35282
MIR31HG
MIR491
FAM138C
SCARNA8
CDKN2B-AS1
C9orf146
WASH1
MIR3152
MIR4473
MIR4665
MIR4474

Genes in Wide Peak

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

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

Genes
BCL2
SS18
MALT1
ZNF521
hsa-mir-122
hsa-mir-4320
hsa-mir-1539
hsa-mir-4319
hsa-mir-924
hsa-mir-4318
hsa-mir-187
hsa-mir-302f
hsa-mir-320c-2
hsa-mir-1-2
hsa-mir-320c-1
hsa-mir-3156-2
hsa-mir-4317
ADCYAP1
AQP4
ATP5A1
C18orf1
CDH2
CDH7
CETN1
CIDEA
CYB5A
DCC
DSC1
DSC2
DSC3
DSG1
DSG2
DSG3
DTNA
FECH
KDSR
GALR1
GALNT1
GATA6
GNAL
GRP
IMPA2
LAMA3
LMAN1
SMAD2
SMAD4
SMAD7
MBD1
MBP
MC2R
MC4R
MC5R
ME2
MEP1B
MYO5B
NARS
NDUFV2
NFATC1
NPC1
SERPINB2
ATP8B1
SERPINB5
SERPINB8
SERPINB10
SERPINB13
PIK3C3
PMAIP1
MAPK4
PTPN2
PTPRM
RAB27B
RBBP8
RIT2
ROCK1
RPL17
SERPINB3
SERPINB4
SLC14A1
SNRPD1
SYT4
TAF4B
TCF4
TGIF1
TTR
TYMS
YES1
ZFP161
ZNF24
ZNF236
SLC14A2
SERPINB7
NOL4
RNMT
MYOM1
NAPG
RIOK3
TNFRSF11A
MBD2
PSTPIP2
PIAS2
USP14
CTDP1
VAPA
DLGAP1
SOCS6
B4GALT6
TXNL1
LIPG
ONECUT2
VPS4B
ZNF516
LPIN2
CTIF
THOC1
PPP4R1
TSHZ1
NDC80
ACAA2
MYL12A
SLMO1
CD226
ZNF271
TXNL4A
RALBP1
AFG3L2
MAPRE2
RAB31
POLI
ADNP2
TRAPPC8
EPB41L3
PHLPP1
ANKRD12
CCDC165
NEDD4L
WDR7
SMCHD1
PIGN
SLC39A6
RTTN
TPGS2
SETBP1
KCNG2
CABYR
SNORD58B
SNORD58A
CLUL1
SALL3
CDH20
CDH19
TIMM21
ST8SIA5
C18orf8
RAX
CXXC1
ST8SIA3
IER3IP1
TCEB3B
MEX3C
RNF138
TMX3
DYM
ZCCHC2
RNF125
MOCOS
CEP192
RPRD1A
ZNF532
ELP2
IMPACT
ELAC1
ENOSF1
ZNF407
CNDP2
LINC00470
CELF4
SPIRE1
PSMG2
TWSG1
CHMP1B
MIB1
KIAA1328
KLHL14
KIAA1468
EPG5
HRH4
PIEZO2
CTAGE1
FAM59A
METTL4
MPPE1
ARHGAP28
CCDC102B
RBFA
CEP76
GREB1L
PQLC1
FHOD3
CCDC68
ASXL3
COLEC12
NETO1
SEH1L
KATNAL2
CHST9
C18orf21
MRO
EMILIN2
HDHD2
TXNDC2
ZNF397
PARD6G
TUBB6
CNDP1
TMEM241
SERPINB12
SERPINB11
SEC11C
L3MBTL4
CABLES1
DSEL
MYL12B
ESCO1
OSBPL1A
HAUS1
ALPK2
FAM210A
LOXHD1
INO80C
TTC39C
FAM69C
PSMA8
STARD6
C18orf25
CCBE1
CBLN2
MCART2
DSG4
CHST9-AS1
ANKRD29
APCDD1
LINC00526
ZNF519
C18orf54
TCEB3C
ABHD3
FBXO15
RAB12
LOC201477
ZBTB7C
SKA1
CCDC11
DOK6
RNF152
LINC00305
ZNF396
LOC284215
LAMA1
CYP4F35P
KCTD1
C18orf26
BOD1P
LOC284260
SIGLEC15
ZADH2
C18orf62
LOC284276
HMSD
LOC284294
LOC339290
LRRC30
LOC339298
CPLX4
ANKRD30B
C18orf34
ATP9B
POTEC
LOC390858
LOC400643
LOC400654
LOC400655
LOC400657
MIR1-2
MIR122
MIR133A1
MIR187
CXADRP3
ANKRD20A5P
HSBP1L1
WBP11P1
RNF165
C18orf56
C18orf32
KC6
C18orf42
LOC643542
C18orf63
LOC644669
CBX3P2
LOC645355
TMEM200C
LOC647946
FLJ35776
SCARNA17
SNORA37
ROCK1P1
LOC727896
LOC728606
TCEB3CL
LOC729950
ZSCAN30
SNORD58C
LOC100130480
LOC100130522
LOC100131655
LOC100192426
LOC100287225
LOC100288122
MIR302F
MIR320C1
MIR320C2
MIR1539
MIR4319
MIR4317
MIR4318
MIR4320
MIR3156-2
LOC100505474
LOC100505549
LOC100505776
LOC100505817
LOC100506888
RPL17-C18ORF32
MIR4526
MIR4741
MIR3976
MIR3975
MIR4529
MIR3591
MIR4743
MIR4744
LOC100652770

Arm-level results

Table 3. Get Full Table Arm-level significance table - 18 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.02 | 0.811 | 0.857 | 0.03 | 1.53 | 0.211
1q | 1955 | 0.04 | 2.21 | 0.0894 | 0.01 | -0.29 | 0.995
2p | 924 | 0.00 | -2.55 | 0.996 | 0.01 | -1.76 | 0.995
2q | 1556 | 0.01 | -1.51 | 0.996 | 0.01 | -1.01 | 0.995
3p | 1062 | 0.08 | 2.66 | 0.0311 | 0.01 | -1.48 | 0.995
3q | 1139 | 0.11 | 4.56 | 2.58e-05 | 0.01 | -1.81 | 0.995
4p | 489 | 0.03 | -1.39 | 0.996 | 0.02 | -1.74 | 0.995
4q | 1049 | 0.03 | -0.773 | 0.996 | 0.01 | -2.01 | 0.995
5p | 270 | 0.01 | -2.66 | 0.996 | 0.02 | -1.98 | 0.995
5q | 1427 | 0.01 | -1.63 | 0.996 | 0.03 | 0.262 | 0.835
6p | 1173 | 0.00 | -2.33 | 0.996 | 0.03 | -0.182 | 0.995
6q | 839 | 0.00 | -2.55 | 0.996 | 0.07 | 1.33 | 0.28
7p | 641 | 0.17 | 7.04 | 1.28e-11 | 0.00 | -2.53 | 0.995
7q | 1277 | 0.15 | 8.14 | 8.88e-15 | 0.00 | -2.1 | 0.995
8p | 580 | 0.09 | 1.97 | 0.131 | 0.39 | 18.8 | 0
8q | 859 | 0.18 | 7.79 | 6.88e-14 | 0.08 | 1.97 | 0.0975
9p | 422 | 0.04 | -0.677 | 0.996 | 0.04 | -0.677 | 0.995
9q | 1113 | 0.07 | 1.94 | 0.131 | 0.02 | -1.01 | 0.995
10p | 409 | 0.04 | -0.992 | 0.996 | 0.07 | 0.75 | 0.604
10q | 1268 | 0.03 | -0.299 | 0.996 | 0.09 | 3.69 | 0.000631
11p | 862 | 0.03 | -1.02 | 0.996 | 0.00 | -2.58 | 0.995
11q | 1515 | 0.03 | 0.416 | 0.996 | 0.00 | -2.03 | 0.995
12p | 575 | 0.01 | -2.34 | 0.996 | 0.07 | 1.29 | 0.284
12q | 1447 | 0.02 | -0.622 | 0.996 | 0.03 | 0.33 | 0.824
13q | 654 | 0.01 | -2.18 | 0.996 | 0.13 | 4.84 | 4.31e-06
14q | 1341 | 0.00 | -2.18 | 0.996 | 0.04 | 0.557 | 0.722
15q | 1355 | 0.01 | -1.67 | 0.996 | 0.06 | 2 | 0.0975
16p | 872 | 0.06 | 0.792 | 0.857 | 0.07 | 1.57 | 0.21
16q | 702 | 0.03 | -0.758 | 0.996 | 0.20 | 8.57 | 0
17p | 683 | 0.02 | -1.74 | 0.996 | 0.13 | 4.95 | 2.98e-06
17q | 1592 | 0.01 | -1.45 | 0.996 | 0.03 | 0.075 | 0.94
18p | 143 | 0.02 | -1.74 | 0.996 | 0.17 | 5.5 | 1.92e-07
18q | 446 | 0.02 | -1.8 | 0.996 | 0.21 | 8.38 | 0
19p | 995 | 0.01 | -1.65 | 0.996 | 0.02 | -1.25 | 0.995
19q | 1709 | 0.01 | -0.761 | 0.996 | 0.02 | -0.223 | 0.995
20p | 355 | 0.01 | -2.2 | 0.996 | 0.04 | -0.822 | 0.995
20q | 753 | 0.03 | -0.712 | 0.996 | 0.02 | -1.47 | 0.995
21q | 509 | 0.02 | -1.71 | 0.996 | 0.03 | -0.997 | 0.995
22q | 921 | 0.01 | -2.03 | 0.996 | 0.09 | 2.73 | 0.0159
Xq | 1312 | 0.00 | -2.21 | 0.996 | 0.04 | 0.502 | 0.724

Methods & Data
Input
Description

- Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

- Markers File: The markers file identifies the marker names and positions of the markers in the original dataset (before segmentation). It is a three column, tab-delimited file with an optional header. The column headers are: (1) Marker Name, (2) Chromosome, (3) Marker Position (in bases).

- Reference Genome: The reference genome file contains information about the location of genes and cytobands on a given build of the genome. Reference genome files are created in Matlab and are not viewable with a text editor.

- CNV Files: There are two options for the cnv file. The first option allows CNVs to be identified by marker name. The second option allows the CNVs to be identified by genomic location. Option #1: A two column, tab-delimited file with an optional header row. The marker names given in this file must match the marker names given in the markers file. The CNV identifiers are for user use and can be arbitrary. The column headers are: (1) Marker Name, (2) CNV Identifier. Option #2: A 6 column, tab-delimited file with an optional header row. The 'CNV Identifier' is for user use and can be arbitrary. 'Narrow Region Start' and 'Narrow Region End' are also not used. The column headers are: (1) CNV Identifier, (2) Chromosome, (3) Narrow Region Start, (4) Narrow Region End, (5) Wide Region Start, (6) Wide Region End

- Amplification Threshold: Threshold for copy number amplifications. Regions with a log2 ratio above this value are considered amplified.

- Deletion Threshold: Threshold for copy number deletions. Regions with a log2 ratio below the negative of this value are considered deletions.

- Cap Values: Minimum and maximum cap values on analyzed data. Regions with a log2 ratio greater than the cap are set to the cap value; regions with a log2 ratio less than -cap value are set to -cap. Values must be positive.

- Broad Length Cutoff: Threshold used to distinguish broad from focal events, given in units of fraction of chromosome arm.

- Remove X-Chromosome: Flag indicating whether to remove data from the X-chromosome before analysis. Allowed values= {1,0} (1: Remove X-Chromosome, 0: Do not remove X-Chromosome.

- Confidence Level: Confidence level used to calculate the region containing a driver.

- Join Segment Size: Smallest number of markers to allow in segments from the segmented data. Segments that contain fewer than this number of markers are joined to the neighboring segment that is closest in copy number.

- Arm Level Peel Off: Flag set to enable arm-level peel-off of events during peak definition. The arm-level peel-off enhancement to the arbitrated peel-off method assigns all events in the same chromosome arm of the same sample to a single peak. It is useful when peaks are split by noise or chromothripsis. Allowed values= {1,0} (1: Use arm level peel off, 0: Use normal arbitrated peel-off).

- Maximum Sample Segments: Maximum number of segments allowed for a sample in the input data. Samples with more segments than this threshold are excluded from the analysis.

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/PRAD/1709016/2.GDAC_MergeDataFiles.Finished/PRAD.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

- Markers File = /xchip/cga/reference/gistic2/genome.info.6.0_hg19.na31_minus_frequent_nan_probes_sorted_2.1.txt

- Reference Genome = /xchip/cga/reference/gistic2/hg19_with_miR_20120227.mat

- CNV Files = /xchip/cga/reference/gistic2/CNV.hg19.bypos.111213.txt

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 4. Get Full Table First 10 out of 152 Input Tumor Samples.

Tumor Sample Names
TCGA-CH-5737-01A-11D-1574-01
TCGA-CH-5738-01A-11D-1574-01
TCGA-CH-5739-01A-11D-1574-01
TCGA-CH-5740-01A-11D-1574-01
TCGA-CH-5741-01A-11D-1574-01
TCGA-CH-5743-01A-21D-1574-01
TCGA-CH-5744-01A-11D-1574-01
TCGA-CH-5746-01A-11D-1574-01
TCGA-CH-5748-01A-11D-1574-01
TCGA-CH-5750-01A-11D-1574-01

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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