Sarcoma: 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 29 tumor samples used in this analysis: 12 significant arm-level results, 11 significant focal amplifications, and 17 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 - 11 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
--- | --- | --- | --- | ---
12q14.1 | 1.4484e-20 | 1.4484e-20 | chr12:58104883-58163019 | 8
6p21.1 | 0.0070848 | 0.0070848 | chr6:41698135-42692619 | 17
12p13.32 | 0.063418 | 0.063418 | chr12:4747451-5351735 | 6
5p14.1 | 0.023365 | 0.067484 | chr5:24837900-24942127 | 1
6q25.1 | 0.095445 | 0.095445 | chr6:148792599-150644383 | 22
17p11.2 | 0.12887 | 0.12887 | chr17:8948105-25270799 | 147
7p15.3 | 0.14919 | 0.14919 | chr7:18906542-36312081 | 136
19p13.2 | 0.14919 | 0.14919 | chr19:9576119-11301146 | 67
4p15.2 | 0.1696 | 0.1696 | chr4:25503978-26095818 | 3
1q24.3 | 0.19479 | 0.19479 | chr1:171188058-172510147 | 16
5p14.2 | 0.0070848 | 0.27354 | chr5:23432984-23709942 | 1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q14.1.

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

Genes
CDK4
CYP27B1
METTL1
TSPAN31
OS9
MARCH9
AGAP2
LOC100130776

Genes in Wide Peak

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

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

Genes
CCND3
TFEB
BYSL
GUCA1A
GUCA1B
PGC
PRPH2
MED20
FRS3
UBR2
USP49
PRICKLE4
MRPS10
TRERF1
TAF8
C6orf132
TOMM6

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p13.32.

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

Genes
KCNA1
KCNA5
KCNA6
NDUFA9
AKAP3
GALNT8

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p14.1.

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

Genes
LOC340107

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q25.1.

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

Genes
PCMT1
LATS1
UST
KATNA1
TAB2
SASH1
ULBP3
ULBP2
ULBP1
PPP1R14C
LRP11
PPIL4
C6orf72
RAET1E
RAET1L
ZC3H12D
NUP43
RAET1G
SUMO4
RAET1K
LOC100128176
LOC100652739

Genes in Wide Peak

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

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

Genes
MAP2K4
GAS7
hsa-mir-1180
hsa-mir-33b
hsa-mir-1288
hsa-mir-548h-3
hsa-mir-744
ADORA2B
ALDH3A1
ALDH3A2
COX10
DNAH9
DRG2
FOXO3B
FLII
KCNJ12
LLGL1
MEIS3P1
MFAP4
MYH1
MYH2
MYH3
MYH4
MYH8
PMP22
MAPK7
MAP2K3
PRPSAP2
RCVRN
SCO1
SHMT1
SREBF1
TOP3A
UBB
ZNF18
RNF112
COPS3
MYH13
TMEM11
GLP2R
NTN1
STX8
PIGL
NCOR1
ULK2
CCDC144A
ARHGAP44
HS3ST3B1
HS3ST3A1
PEMT
FBXW10
TRIM16
RAI1
GRAP
AKAP10
EPN2
MPRIP
USP22
TNFRSF13B
DHRS7B
SNORD49A
B9D1
FAM18B1
MYO15A
TRPV2
RASD1
ALKBH5
TTC19
MED9
SLC47A1
NT5M
C17orf48
ZNF286A
ZNF287
ZNF624
ELAC2
TEKT3
C17orf39
FAM106A
LRRC48
MGC12916
ATPAF2
SPECC1
MYOCD
CDRT7
CDRT15P1
USP43
C17orf76-AS1
ZSWIM7
SMCR7
SLC5A10
SMCR5
SMCR8
SMCR9
TOM1L2
SLC47A2
CDRT15
WDR16
TRIM16L
USP32P1
DHRS7C
FAM18B2
CENPV
FLCN
PLD6
USP32P2
TBC1D28
CDRT15L2
C17orf103
FLJ34690
CDRT4
CCDC144B
FAM27L
FLJ36000
LGALS9B
CCDC144NL
LOC339240
C17orf51
CCDC144C
TBC1D26
CDRT1
TMEM220
SHISA6
FAM211A
KRT16P2
GRAPL
PIRT
CDRT15P2
FAM83G
KRT16P3
EVPLL
LGALS9C
SNORA59B
SNORA59A
SNORD49B
SNORD65
MIR33B
ZNF286B
MIR744
FAM106CP
KCNJ18
LOC100289255
MIR1288
MIR1180
MTRNR2L1
FAM18B2-CDRT4
MIR4731

Genes in Wide Peak

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

Table S7. 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-548n
hsa-mir-550-2
hsa-mir-550-1
hsa-mir-196b
hsa-mir-148a
hsa-mir-1183
hsa-mir-3146
ADCYAP1R1
AQP1
SEPT7
CHN2
CLK2P
CRHR2
DFNA5
EVX1
GARS
GHRHR
HOXA1
HOXA2
HOXA3
HOXA4
HOXA5
HOXA6
HOXA7
HOXA10
IL6
ITGB8
NPY
PDE1C
RP9
SP4
TWIST1
DNAH11
TAX1BP1
SKAP2
CREB5
NFE2L3
HDAC9
RAPGEF5
SCRN1
KIAA0087
TRIL
NOD1
GPNMB
IGF2BP3
PPP1R17
NUPL2
HIBADH
INMT
FKBP9
CBX3
AVL9
DPY19L1
LSM5
KBTBD2
OSBPL3
BBS9
SNX10
TRA2A
NT5C3
MPP6
CYCS
CPVL
TOMM7
FKBP14
CDCA7L
KLHL7
STK31
TBX20
NEUROD6
NPVF
HERPUD2
GGCT
EEPD1
FAM188B
FAM126A
PLEKHA8
CCDC126
C7orf30
C7orf31
BMPER
TWISTNB
SP8
HOXA11-AS1
DKFZP586I1420
C7orf41
PRR15
FERD3L
RPL23P8
CCDC129
ZNRF2
TMEM196
STEAP1B
RPS2P32
C7orf71
ABCB5
C7orf46
MACC1
NPSR1
LOC401320
LOC401321
LOC401324
AAA1
MIR148A
LOC441204
ZNRF2P1
RP9P
DPY19L2P3
MIR196B
DPY19L2P1
WIPF3
LOC646762
SNORD93
MIR550A1
MIR550A2
JAZF1-AS1
DPY19L1P1
LOC100130673
LOC100133311
ZNRF2P2
HOTTIP
MIR3146
MIR550B2
MIR550B1
LOC100506178
HOTAIRM1
LOC100506497
INMT-FAM188B
HOXA10-HOXA9
MIR550A3
KLHL7-AS1

Genes in Wide Peak

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

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

Genes
SMARCA4
hsa-mir-199a-1
hsa-mir-638
hsa-mir-1238
hsa-mir-1181
hsa-mir-4322
CDKN2D
DNM2
DNMT1
ICAM1
ICAM3
ICAM4
ILF3
LDLR
P2RY11
PDE4A
PIN1
ICAM5
TYK2
ZNF121
EIF3G
S1PR2
KEAP1
AP1M2
CARM1
TMED1
CDC37
KANK2
COL5A3
RDH8
MRPL4
S1PR5
ZNF562
FBXL12
C19orf66
PPAN
SLC44A2
UBL5
KRI1
YIPF2
ZNF426
QTRT1
ANGPTL6
ATG4D
C19orf52
ZNF561
OLFM2
FDX1L
RAVER1
LOC147727
ZNF560
SPC24
ZNF846
C19orf38
LOC284385
C3P1
MIR199A1
SNORD105
PPAN-P2RY11
MIR638
ZNF812
SNORD105B
ZGLP1
MIR1181
MIR1238
MIR4322
MIR4748

Genes in Wide Peak

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

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

Genes
SLC34A2
SEL1L3
C4orf52

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q24.3.

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

Genes
hsa-mir-199a-2
FMO1
FMO4
MYOC
PIGC
TOP1P1
VAMP4
PRRC2C
DNM3
C1orf9
METTL13
C1orf105
MIR199A2
MIR214
MIR3120
DNM3OS

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p14.2.

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

Genes
PRDM9

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 - 17 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
--- | --- | --- | --- | ---
13q14.2 | 0.00077814 | 0.00077814 | chr13:48833767-49064807 | 2
9p21.3 | 0.0015041 | 0.0015041 | chr9:21865498-22448737 | 4
2q37.3 | 0.0029586 | 0.0029586 | chr2:242162274-243199373 | 17
Xq21.1 | 0.003065 | 0.003065 | chrX:76710176-77102528 | 1
Xq28 | 0.026218 | 0.027178 | chrX:147107975-149615811 | 15
12p12.3 | 0.048906 | 0.048906 | chr12:1-39688977 | 339
21q22.3 | 0.06465 | 0.064052 | chr21:46289952-48129895 | 29
11q22.3 | 0.12242 | 0.12242 | chr11:76060285-135006516 | 440
11p15.4 | 0.13543 | 0.13584 | chr11:1-15988821 | 302
17p13.1 | 0.16078 | 0.14688 | chr17:7613709-7744654 | 2
4q35.1 | 0.16769 | 0.16769 | chr4:54241403-191154276 | 616
17q25.3 | 0.17141 | 0.17141 | chr17:80331848-80617015 | 7
1q44 | 0.1748 | 0.1748 | chr1:190593650-249250621 | 488
5q23.3 | 0.18917 | 0.19141 | chr5:126385194-180915260 | 537
19q13.32 | 0.20445 | 0.20587 | chr19:42823902-59128983 | 685
3q24 | 0.20697 | 0.20697 | chr3:9741309-198022430 | 1246
15q13.2 | 0.20697 | 0.20697 | chr15:1-81251100 | 673

Genes in Wide Peak

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

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

Genes
RB1
LPAR6

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
C9orf53
CDKN2B-AS1

Genes in Wide Peak

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

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

Genes
hsa-mir-3133
BOK
DTYMK
HDLBP
SEPT2
PDCD1
FARP2
STK25
ATG4B
THAP4
GAL3ST2
ING5
NEU4
CXXC11
D2HGDH
LOC728323
BOK-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq21.1.

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

Genes
ATRX

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq28.

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

Genes
hsa-mir-2114
AFF2
IDS
MAGEA8
MAGEA9
MAGEA11
TMEM185A
CXorf40A
CXorf40B
MAGEA9B
HSFX2
LOC100131434
LOC100272228
MIR2114
HSFX1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p12.3.

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

Genes
CCND2
ETV6
KRAS
KDM5A
ZNF384
hsa-mir-4302
hsa-mir-920
hsa-mir-614
hsa-mir-613
hsa-mir-1244-3
hsa-mir-141
A2M
A2MP1
APOBEC1
ARHGDIB
ART4
BCAT1
BICD1
C1R
C1S
C3AR1
CACNA1C
CD4
CD9
CD27
CD69
CDKN1B
CHD4
CREBL2
DDX11
ATN1
PHC1
EMP1
ENO2
EPS8
FGF6
FKBP4
FOXM1
GAPDH
GNB3
GPR19
GRIN2B
GUCY2C
GYS2
IAPP
ITPR2
KCNA1
KCNA5
KCNA6
KCNJ8
KLRB1
KLRC1
KLRC2
KLRC3
KLRD1
LAG3
LDHB
LRMP
LRP6
LTBR
M6PR
MGP
MGST1
NDUFA9
NINJ2
NOP2
NTF3
OLR1
PDE3A
PDE6H
PIK3C2G
PKP2
PRB1
PRB3
PRB4
PRH1
PRH2
PTHLH
PTMS
PTPN6
PTPRO
PEX5
PZP
RAD52
RECQL
SCNN1A
ST8SIA1
SLC2A3
SLC6A12
SLC6A13
SLCO1A2
SOX5
VAMP1
TEAD4
TNFRSF1A
TPI1
TULP3
VWF
FGF23
MFAP5
USP5
MLF2
SSPN
KLRC4
PPFIBP1
CSDA
DYRK4
GPRC5A
CD163
MED21
GDF3
CLSTN3
KIAA0528
NCAPD2
CLEC2B
DNM1L
ABCC9
LPCAT3
KLRG1
LRRC23
EMG1
IPO8
LEPREL2
AKAP3
SLCO1B1
RAD51AP1
KLRAP1
TSPAN9
STRAP
RASSF8
PRR4
PHB2
KLRK1
STK38L
ERC1
GABARAPL1
IFFO1
NECAP1
FGFR1OP2
CLEC4E
GALNT8
GPR162
SLCO1B3
CLEC2D
COPS7A
TAS2R9
TAS2R8
TAS2R7
TAS2R13
TAS2R10
TAS2R14
CLEC4A
HEBP1
GOLT1B
YARS2
DERA
ING4
DDX47
MRPL51
CLEC1B
CLEC1A
C1RL
ERGIC2
KLRF1
WBP11
TM7SF3
SLCO1C1
PLEKHA5
MANSC1
TAPBPL
MAGOHB
FAM90A1
C12orf35
PLEKHG6
CASC1
CCDC91
STYK1
ETNK1
GPRC5D
FAR2
ASUN
ATF7IP
H2AFJ
FOXJ2
ITFG2
LMO3
CMAS
PRMT8
ARNTL2
PARP11
ANO2
C12orf4
C12orf5
LPAR5
AICDA
RIMKLB
KLHDC5
KIAA1467
FAM60A
MRPS35
CLEC7A
WNK1
CAPRIN2
BHLHE41
BCL2L14
ADIPOR2
RERGL
FLJ13224
PLBD1
PYROXD1
NANOG
C12orf39
DUSP16
WNT5B
APOLD1
GSG1
CDCA3
C12orf32
NRIP2
RBP5
TMTC1
CCDC77
ACRBP
SPSB2
EFCAB4B
ALG10
RERG
PLCZ1
HTR7P1
CACNA2D4
CAPZA3
CLEC6A
C12orf57
LOH12CR1
C12orf59
HIST4H4
ERP27
FGD4
AEBP2
SLC2A14
ALG10B
LINC00477
LYRM5
CPNE8
A2ML1
LOC144571
C12orf60
FBXL14
CLEC12A
CLECL1
IFLTD1
DENND5B
CLEC4C
DSTNP2
AMN1
C12orf77
C12orf53
DCP1B
C12orf33
METTL20
TAS2R43
TAS2R31
TAS2R46
TAS2R30
TAS2R19
TAS2R20
TAS2R50
MATL2963
CD163L1
RPL13P5
B4GALNT3
CLEC9A
C12orf36
LOC283440
CLEC4D
LOC338817
SLCO1B7
C12orf70
OVCH1
SYT10
ACSM4
TAS2R42
DPPA3
NANOGNB
LOC374443
CLEC2A
CLEC12B
RPL13AP20
REP15
LOC389634
MIR141
MIR200C
IQSEC3
ZNF705A
FAM66C
DDX12P
C12orf69
H3F3C
TSPAN11
LOH12CR2
LOC574538
POU5F1P3
LOC642846
FAM86FP
PRB2
LRTM2
SCARNA12
SCARNA11
FAM138D
LOC678655
SCARNA10
MIR613
MIR614
SKP1P2
C12orf71
SLC15A5
MIR920
LOC100129361
LOC100271702
MANSC4
LOC100287314
LOC100288778
LOC100292680
MIR1244-1
MIR1244-3
MIR1244-2
MIR4302
KLRF2
LOC100499405
MIR3649
LOC100506314
LOC100506393
LOC100506451
LOC100506660
LOC100507424
KLRC4-KLRK1
PRH1-PRR4
MIR3974
LOC100652846

Genes in Wide Peak

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

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

Genes
ADARB1
COL6A1
COL6A2
PRMT2
ITGB2
LSS
PCNT
S100B
SLC19A1
MCM3AP
FTCD
DIP2A
POFUT2
PCBP3
C21orf58
YBEY
COL18A1
C21orf56
C21orf67
FAM207A
MCM3AP-AS1
LINC00315
LINC00162
COL18A1-AS1
LOC642852
LINC00163
SSR4P1
LOC100129027
LOC100505746

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q22.3.

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

Genes
BIRC3
ATM
CBL
DDX6
DDX10
FLI1
MLL
PAFAH1B2
POU2AF1
SDHD
PICALM
PCSK7
ARHGEF12
MAML2
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
hsa-mir-1260b
hsa-mir-548l
hsa-mir-1304
hsa-mir-1261
hsa-mir-3166
hsa-mir-4300
hsa-mir-708
ACAT1
ACRV1
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CAPN5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CTSC
CHEK1
CLNS1A
CRYAB
DLAT
DLG2
DPAGT1
DRD2
ETS1
FDX1
FUT4
SLC37A4
LRRC32
GRIA4
GRIK4
GRM5
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
MRE11A
MTNR1B
MYO7A
NCAM1
NDUFC2
NFRKB
NNMT
NPAT
NRGN
OMP
OPCML
PAK1
PGR
PPP2R1B
PRCP
PRKRIR
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
THRSP
THY1
TRPC6
TYR
UPK2
ZBTB16
ZNF202
CUL5
FZD4
BARX2
OR7E2P
JRKL
EED
ZNF259
MTMR2
USP2
HTR3B
ZW10
MMP20
UBE4A
MED17
EI24
FEZ1
CEP57
ARHGAP32
GAB2
C2CD2L
NAALAD2
RBM7
MPZL2
YAP1
HYOU1
ATP5L
ME3
GPR83
SRSF8
ADAMTS8
PRSS23
TREH
CEP164
IGSF9B
ENDOD1
EXPH5
PHLDB1
SIK2
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
RAB38
CADM1
PANX1
POU2F3
TSKU
HINFP
REXO2
ODZ4
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
CHORDC1
ACAD8
B3GAT1
RAB30
DCPS
C11orf54
C11orf67
ZBTB44
THYN1
DDX25
NOX4
NTM
CDON
SIDT2
TRAPPC4
C11orf73
CWC15
PCF11
RSF1
SPA17
FXYD6
CNTN5
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
SYTL2
ANKRD49
TTC12
C11orf57
ACER3
ELMOD1
FOXRED1
KDM4D
SCN3B
VPS11
TMEM126B
TEX12
CRTAM
TMPRSS4
IFT46
C11orf75
C11orf30
PRDM10
TRIM49
DSCAML1
GRAMD1B
USP35
KIAA1377
ARHGAP20
USP28
CREBZF
CARD18
CCDC90B
CCDC81
AASDHPPT
PKNOX2
TP53AIP1
MMP27
ABCG4
ROBO3
C11orf1
TMEM135
KCTD14
ALG8
TAF1D
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
NARS2
CCDC82
ALG9
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
JAM3
BCO2
TMEM133
TMPRSS13
TMEM126A
DCUN1D5
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
C11orf70
DIXDC1
KIAA1731
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
INTS4
VPS26B
GLB1L3
TIRAP
CARD16
C1QTNF5
TMEM123
PANX3
APOA5
SLC36A4
FAT3
TRIM64
TMEM45B
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
FAM76B
SESN3
PIWIL4
ARHGAP42
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
AMOTL1
CCDC67
PATE1
C11orf65
ADAMTS15
B3GNT6
MPZL3
FOLH1B
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
GDPD4
C11orf82
CCDC83
HEPACAM
OAF
FAM181B
CCDC89
ANGPTL5
ANKK1
RNF214
AQP11
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
KCTD21
CCDC84
TMEM225
OR8D4
ANKRD42
C11orf53
LOC341056
HEPHL1
C11orf34
VSTM5
GUCY2E
TRIM77P
FOLR4
KDM4DL
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
LOC399939
LOC399940
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
LINC00167
SCARNA9
HEPN1
TRIM64B
TRIM53P
TRIM49L2
UBTFL1
LOC643037
LOC643733
LOC643923
CLDN25
LOC649133
RPL23AP64
SNORA8
SNORA1
SNORA18
SNORA40
SNORA25
SNORA32
SNORD5
SNORD6
TRIM49L1
MIR708
LOC100128239
LOC100132078
PATE3
LOC100288077
LOC100288346
MIR1304
SNORA70E
BACE1-AS
MIR4300
MIR4301
MIR3167
MIR1260B
LOC100499227
MIR3920
MIR3656
LOC100506233
LOC100506368
CASP12
LOC100507392
LOC100526771
HSPB2-C11orf52
NDUFC2-KCTD14
FXYD6-FXYD2
MIR4697
MIR4490
MIR4493
MIR4491
MIR4492
MIR4693
LOC100652768

Genes in Wide Peak

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

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

Genes
CARS
HRAS
LMO1
NUP98
hsa-mir-4299
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
ADM
AP2A2
AMPD3
APBB1
RHOG
ARNTL
ART1
ASCL2
CALCA
CALCB
CCKBR
CD81
CD151
CDKN1C
TPP1
CNGA4
COPB1
CTSD
DRD4
DUSP8
EIF4G2
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INS
IRF7
KCNQ1
LSP1
MUC2
MUC6
NAP1L4
SLC22A18
SLC22A18AS
PDE3B
POLR2L
PSMA1
PSMD13
PTH
RNH1
MRPL23
RPL27A
RPLP2
RRM1
SCT
SMPD1
TRIM21
ST5
STIM1
TAF10
TALDO1
TEAD1
TH
TSPAN4
TNNI2
TNNT3
TRPC2
PHLDA2
TUB
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
PPFIBP2
IFITM1
OR6A2
DCHS1
EIF3F
BRSK2
MICAL2
CTR9
TRIM66
TSPAN32
TSSC4
MRVI1
TRIM22
IFITM3
SPON1
DEAF1
IPO7
IFITM2
TRIM3
OR7E12P
LYVE1
KCNQ1OT1
PKP3
RRAS2
SWAP70
DENND5A
RRP8
SIRT3
OR52A1
ARFIP2
OR5E1P
OR10A3
FXC1
DKK3
RBMXL2
PGAP2
C11orf21
TRPM5
UBQLN3
RNF141
IGF2-AS1
BET1L
CEND1
CYB5R2
TRIM34
CDHR5
TOLLIP
USP47
TRIM68
PIDD
KCNQ1DN
PARVA
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
CHRNA10
PNPLA2
PHRF1
SCUBE2
ZBED5
SIGIRR
RIC8A
MRPL17
EPS8L2
STK33
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
MOB2
SBF2
FAM160A2
FAR1
BTBD10
MICALCL
TRIM5
SYT8
PRKCDBP
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
TRIM78P
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR5P2
OR5P3
CYP2R1
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
LOC143666
OR10A5
OR2AG1
DNHD1
SCGB1C1
C11orf42
NLRP6
NS3BP
OR56B4
LOC255512
OR52B2
C11orf35
OR51F1
OR51B5
KRT8P41
LOC283104
CSNK2A1P
OR51V1
H19
EFCAB4A
TMEM80
OR10A4
OLFML1
LOC283299
C11orf36
NLRP10
NLRP14
ANO9
LOC338651
B4GALNT4
OR52L1
OR2AG2
OR52B6
OR10A2
OVCH2
PDDC1
GALNTL4
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR56B1
GVINP1
INSC
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440028
TRIM6-TRIM34
MIR483
SNORA3
SNORA52
LOC644656
RASSF10
LOC650368
LOC653486
SNORA23
SNORA45
SNORA54
SNORD97
INS-IGF2
MUC5B
LOC729013
MIR675
MRVI1-AS1
FAM99B
LOC100133161
MRPL23-AS1
MIR4298
MIR4299
MTRNR2L8
MIR210HG
LOC100506305
MIR4686
MIR4485
MIR4687

Genes in Wide Peak

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

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

Genes
RPL29P2
DNAH2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.1.

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

Genes
IL2
KDR
KIT
PDGFRA
RAP1GDS1
DUX4
CHIC2
TET2
FBXW7
FIP1L1
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
hsa-mir-1979
hsa-mir-3140
hsa-mir-548g
hsa-mir-3139
hsa-mir-2054
hsa-mir-1973
hsa-mir-577
hsa-mir-1243
hsa-mir-302b
hsa-mir-297
hsa-mir-576
hsa-mir-1255a
hsa-mir-575
hsa-mir-1269
ADH1A
ADH1B
ADH1C
ADH4
ADH5
ADH6
ADH7
AFM
AFP
AGA
ALB
AMBN
ANK2
SLC25A4
ANXA2P1
ANXA3
ANXA5
AREG
ART3
ATOH1
BMP3
BMPR1B
BTC
CAMK2D
CASP3
CASP6
CCNA2
CCNG2
SCARB2
LRBA
CDS1
CLGN
CENPC1
CENPE
CLCN3
CPE
CSN1S1
CSN2
CSN3
CTSO
DCK
DCTD
DMP1
DSPP
EDNRA
EGF
EIF4E
ELF2
ENPEP
EPHA5
EREG
ETFDH
F11
FABP2
ACSL1
FAT1
FGA
FGB
FGF2
FGF5
FGG
FRG1
GAB1
GC
GK2
GK3P
GLRB
GNRHR
GPM6A
GRIA2
GRID2
CXCL1
CXCL2
CXCL3
GRSF1
GUCY1A3
GUCY1B3
GYPA
GYPB
GYPE
H2AFZ
HADH
HMGB2
HNRNPD
HPGD
HSP90AA4P
HSP90AB3P
HTN1
HTN3
IBSP
CFI
IGFBP7
IGJ
IL8
IL15
ING2
CXCL10
IRF2
KLKB1
MAD2L1
SMAD1
MANBA
MGST2
CXCL9
AFF1
NR3C2
MTNR1A
MTTP
MUC7
NDUFC1
NEK1
NFKB1
NKX6-1
NPY1R
NPY2R
NPY5R
PDHA2
PET112
PF4
PF4V1
PITX2
PKD2
PLRG1
EXOSC9
POLR2B
POU4F2
PPEF2
PPAT
PPBP
PPID
PPP3CA
PRKG2
MAPK10
PTPN13
REST
ABCE1
RPL34
RPS3A
MSMO1
CXCL6
CXCL11
CXCL5
SFRP2
SNCA
SPINK2
SPP1
SRP72
STATH
SULT1E1
TACR3
TDO2
TLL1
TLR2
TLR3
TRPC3
UBE2D3
UCP1
UGT2B4
UGT2B7
UGT2B10
UGT2B15
UGT2B17
UGT8
VEGFC
GLRA3
SPARCL1
SMARCA5
SORBS2
PRSS12
USO1
UNC5C
LAMTOR3
PDE5A
SLC4A4
SAP30
INPP4B
HERC3
SNORD73A
STBD1
CDKL2
PAPSS1
LRAT
AIMP1
NDST3
TMPRSS11D
ABCG2
HAND2
ADAMTS3
CLOCK
CEP135
RAPGEF2
MFAP3L
SEC24D
G3BP2
HNRPDL
TSPAN5
ENAM
FAM13A
SPRY1
ANAPC10
PGRMC2
SEC24B
CXCL13
MAB21L2
PAICS
PDLIM5
RRH
UGT2B11
PLK4
HPSE
NMU
SMR3B
NPFFR2
PPBPL2
UGT2A1
CCNI
ADAM29
PRDM5
LSM6
NUDT6
ANXA10
KLHL2
SCRG1
HSPA4L
SEC31A
RUFY3
MMRN1
WDFY3
PALLD
TBC1D9
METAP1
KIAA0922
LPHN3
TRIM2
ANP32C
SLC7A11
CCRN4L
PARM1
FAM149A
RCHY1
ANKRD17
STAP1
FBXO8
DUX2
SMR3A
PPA2
DAPP1
DKK2
INTU
NAAA
COQ2
ARFIP1
SULT1B1
PDLIM3
HPGDS
ZNF330
TMPRSS11E
SPOCK3
MRPS18C
COPS4
AADAT
HSD17B11
LEF1
HERC5
FAM198B
PLAC8
LARP7
EMCN
MYOZ2
ACCN5
GALNT7
NUDT9
NUP54
CLDN22
GAR1
UGT2B28
PCDH18
USP53
DKFZP434I0714
OTUD4
DCHS2
ARHGEF38
ODAM
C4orf27
HERC6
CCDC109B
MARCH1
BANK1
LARP1B
SDAD1
BBS7
UBA6
NEIL3
TMEM144
C4orf43
UFSP2
C4orf21
AP1AR
MAML3
BMP2K
DDX60
CDKN2AIP
ODZ3
TMEM184C
SEPT11
EXOC1
LRP2BP
TMEM165
PDGFC
FSTL5
BDH2
SMARCAD1
MEPE
STOX2
PRDM8
UTP3
INTS12
ANKRD50
KIAA1211
RNF150
KLHL8
PCDH10
KIAA1430
FNIP2
SHROOM3
SH3RF1
METTL14
ENOPH1
PROL1
OSTC
IL21
RXFP1
SPCS3
SCOC
TRAPPC11
NEUROG2
SLC39A8
HHIP
NDST4
AGXT2L1
MRPL1
ELOVL6
NDNF
FAT4
ARSJ
SRD5A3
ARHGAP10
MLF1IP
THAP9
UGT2A3
NBLA00301
GSTCD
MAP9
TNIP3
PHF17
SCD5
DNAJB14
WWC2
FRAS1
NAA15
C4orf29
ALPK1
CXXC4
CEP44
SETD7
PLA2G12A
SLC25A31
RAB33B
ARHGAP24
SNX25
TTC29
MND1
SLC10A7
TKTL2
C4orf17
QRFPR
FAM175A
KIAA1109
NOA1
HOPX
COL25A1
USP38
LNX1
C4orf49
NAA11
AGPAT9
CBR4
PIGY
CABS1
FHDC1
FLJ20021
MGC45800
PRMT10
DDX60L
YTHDC1
NAF1
MOB1B
TIFA
RG9MTD2
TBCK
HELQ
CYP2U1
DDIT4L
WDR17
GDEP
ANTXR2
SCLT1
C4orf33
TMEM155
PABPC4L
ADAD1
ZFP42
LIN54
C4orf32
TMPRSS11B
SPATA4
ARL9
AASDH
PDCL2
C4orf36
TRAM1L1
ENPP6
SLC9B2
ASB5
SLC9B1
ZNF827
SH3D19
PAQR3
C4orf38
C4orf39
THAP6
C4orf26
PPM1K
C4orf45
RASGEF1B
SPATA5
BBS12
DCLK2
TRIM60
FREM3
MMAA
TIGD2
RASSF6
RBM46
SGMS2
GSX2
SYNPO2
C4orf46
TIGD4
TMEM154
TMEM192
RWDD4
CCDC111
TRIML2
CNOT6L
TECRL
C4orf22
LOC255130
EPGN
ELMOD2
NPNT
CCDC110
MFSD8
LOC256880
FDCSP
NAP1L5
LOC285419
CYP4V2
LOC285441
LOC285456
LOC285501
FAM13A-AS1
GPRIN3
COX18
RNF175
C4orf37
CSN1S2AP
CCDC158
TMPRSS11A
LOC339975
TRIML1
LOC340017
PRSS48
SOWAHB
LRIT3
SLC10A6
HSD17B13
ANKRD37
PCNAP1
TMPRSS11F
LOC389247
TRIM61
HELT
LOC401134
SYT14L
TMPRSS11BNL
C4orf40
AMTN
FAM190A
FLJ14186
C4orf3
LOC401164
RPL21P44
FAM92A3
WDFY3-AS2
MIR302A
C4orf11
MTHFD2L
LOC441025
TMEM150C
GUSBP5
HSP90AA6P
C4orf47
DUX4L4
GALNTL6
MIR302B
MIR302C
MIR302D
MIR367
FRG2
CISD2
LOC550112
LOC550113
UGT2A2
LOC641364
LOC641365
LOC641518
SLED1
LOC644145
LOC644248
TMPRSS11GP
CEP170P1
LOC645513
LOC646576
C4orf51
FLJ38576
DUX4L6
DUX4L5
DUX4L3
SNORA24
MIR575
MIR577
MIR578
LINC00290
LOC728175
DUX4L2
CETN4P
FAM160A1
LOC731424
SNHG8
FAM47E
LOC100129858
FTLP10
CLDN24
LOC100144602
PP12613
LOC100288255
MIR1243
MIR2054
MIR1305
MIR1973
CSN1S2BP
MIR3140
MIR4276
LOC100499177
MIR3945
MIR3684
MIR3688-1
LOC100505545
LOC100505702
LOC100505875
LOC100505989
LOC100506013
LOC100506035
LOC100506085
LOC100506122
LOC100506229
LOC100506462
LOC100506564
LOC100506746
LOC100507053
LOC100507096
1/2-SBSRNA4
MIR4453
MIR4799
MIR4450
MIR3688-2
MIR4451
FAM47E-STBD1

Genes in Wide Peak

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

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

Genes
UTS2R
FOXK2
NARF
WDR45L
C17orf62
C17orf101
HEXDC

Genes in Wide Peak

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

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

Genes
ELK4
FH
MDM4
SLC45A3
hsa-mir-3124
hsa-mir-3123
hsa-mir-1537
hsa-mir-1182
hsa-mir-320b-2
hsa-mir-664
hsa-mir-194-1
hsa-mir-3122
hsa-mir-4260
hsa-mir-205
hsa-mir-29b-2
hsa-mir-135b
hsa-mir-1231
hsa-mir-181a-1
hsa-mir-1278
ACTA1
ACTN2
ADORA1
PARP1
ADSS
AGT
ARF1
ATF3
ATP2B4
AVPR1B
C4BPA
C4BPB
CACNA1S
CAPN2
CD34
CENPF
CHI3L1
CHIT1
CHML
LYST
CHRM3
CR1
CR1L
CR2
CSRP1
CTSE
CD55
EIF2D
ELF3
EPHX1
EPRS
ESRRG
F13B
FMOD
NR5A2
GALNT2
GNG4
GPR25
GUK1
H3F3A
CFH
CFHR1
CFHR2
HLX
HNRNPU
HSD11B1
IL10
IRF6
ITPKB
KCNH1
KCNK1
KCNK2
KISS1
LAD1
LAMB3
LBR
LGALS8
MARK1
CD46
MTR
MYBPH
MYOG
PPP1R12B
NEK2
NID1
NVL
CDK18
PFKFB2
PIGR
PIK3C2B
PKP1
PLXNA2
PPP2R5A
PRELP
PROX1
PSEN2
PTPN7
PTPN14
PTPRC
RAB4A
RABIF
RBBP5
REN
RGS1
RGS2
RGS7
RGS13
RNPEP
RYR2
SNRPE
SRP9
TROVE2
AURKAPS1
TARBP1
CNTN2
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TNNI1
TNNT2
TP53BP2
TRAF5
TSNAX
USH2A
WNT9A
ZNF124
SLC30A1
BTG2
HIST3H3
GNPAT
DYRK3
CDC42BPA
PPFIA4
DEGS1
KMO
B3GALT2
RAB7L1
TAF1A
EXO1
FAIM3
MAPKAPK2
GPR37L1
GGPS1
SOX13
IKBKE
TMEM63A
TOMM20
URB2
CEP170
ZC3H11A
TMCC2
LPGAT1
KIF14
AKT3
BPNT1
TIMM17A
LRRN2
ZNF238
LEFTY1
SPHAR
CAPN9
KDM5B
SDCCAG8
CFHR4
CFHR3
IL24
DUSP10
COG2
PLEKHA6
RBM34
KIF21B
NFASC
FBXO28
CAMSAP2
SRGAP2
CRB1
ABCB10
ZNF281
OPN3
PHLDA3
DSTYK
RAB3GAP2
LMOD1
TRIM58
INTS7
AHCTF1
NSL1
OR1C1
OR2M4
OR2L2
OR2L1P
OPTC
OR2T1
RPS6KC1
RNU5F-1
DIEXF
TAF5L
DISC2
DISC1
FLVCR1
UBE2T
CNIH4
PYCR2
NENF
IL19
G0S2
IL20
RRP15
GLRX2
PPPDE1
ADIPOR1
SCCPDH
TRIM17
KCTD3
UCHL5
DTL
CYB5R1
ARID4B
EGLN1
KIAA1383
LAX1
MARC2
SUSD4
KIF26B
GPATCH2
HEATR1
KLHDC8A
ETNK2
TMEM206
YOD1
BATF3
SLC30A10
ZNF692
IARS2
IPO9
HHAT
ENAH
NUP133
RCOR3
C1orf106
SERTAD4
ERO1LB
FMN2
SMYD2
LHX9
ADCK3
ZNF695
GJC2
CAMK1G
SIPA1L2
ZP4
RHOU
KLHL12
LGR6
TFB2M
GREM2
RGS18
NUCKS1
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf116
C1orf35
TTC13
CDC73
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
TRAF3IP3
SH3BP5L
OR2G3
OR2G2
OR2C3
CFHR5
TRIM11
NUAK2
DDX59
RASSF5
MIXL1
C1orf124
FCAMR
OBSCN
NTPCR
EFCAB2
KIAA1804
LINC00260
LINC00467
ZNF496
C1orf198
PPP1R15B
DISP1
WNT3A
NAV1
ANGEL2
IGFN1
TMEM183A
HIST3H2A
LEMD1
ZNF670
NLRP3
SLC26A9
FAM36A
SNAP47
C1orf96
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
ATP6V1G3
DNAH14
OR2B11
ARL8A
SYT2
LOC127841
GOLT1A
WDR64
C1orf131
SPATA17
EDARADD
MRPL55
HIST3H2BB
TATDN3
NEK7
C1orf74
BROX
SLC35F3
LOC148696
LOC148709
PTPRVP
B3GALNT2
MFSD4
PM20D1
C1orf150
LOC148824
CNIH3
LOC149134
SHISA4
EXOC8
RNF187
C1orf227
FAM71A
DENND1B
C1orf55
CNST
C1orf65
PLD5
C1orf100
IBA57
TMEM9
SLC41A1
OR2T6
LOC255654
SYT14
C1orf101
ASPM
PGBD2
OR2L13
OR14A16
LINC00303
LOC284576
LOC284578
LOC284581
HNRNPU-AS1
LIN9
VN1R5
ZNF678
PRSS38
FAM58BP
LOC339529
LOC339535
RD3
OR6F1
OR2W3
OR2T8
OR2T3
KCNT2
OR2T29
IRF2BP2
ZBTB41
MIA3
C1orf95
FAM89A
RPS10P7
C1orf53
TMEM81
CAPN8
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
C1orf140
FAM177B
LOC401980
ZNF847P
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MIR181B1
MIR194-1
MIR205
MIR181A1
MIR215
MIR29B2
MIR29C
RGS21
LOC440704
C1orf186
TRIM67
MAP1LC3C
H3F3AP4
OR2W5
OR13G1
MIR135B
C1orf98
DUSP5P
C1orf133
LOC641515
MIR205HG
FLVCR1-AS1
LOC643723
SNRPD2P2
RPS7P5
LOC646627
TMEM183B
SNORA14B
SNORA36B
SNORA77
SNORA16B
LOC728463
FAM72A
LOC730227
LOC731275
LOC100130093
LOC100130331
LOC100131234
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
MIR1231
MIR1278
MIR664
LINC00184
TSNAX-DISC1
MIR320B2
ZBED6
MIR3123
MIR3124
MIR4260
MIR3122
MIR3620
MIR3916
PROX1-AS1
KDM5B-AS1
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4666A
MIR4677
MIR4735
MIR4671
MIR4427
MIR4742
LINC00538

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q23.3.

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

Genes
CD74
EBF1
ITK
NPM1
PDGFRB
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-3142
hsa-mir-1303
hsa-mir-3141
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
hsa-mir-886
hsa-mir-1289-2
ADRA1B
ADRB2
ANXA6
ATOX1
BNIP1
CAMK2A
CAMLG
CANX
CCNG1
CD14
CDC25C
CDX1
CLTB
CSF1R
CSF2
CSNK1A1
NKX2-5
CTNNA1
DBN1
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EGR1
ETF1
F12
FABP6
FAT2
FBN2
FGF1
FGFR4
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GFRA3
GLRA1
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
HARS
HINT1
HK3
HMMR
HNRNPAB
HNRNPH1
HRH2
HSPA4
HSPA9
NDST1
HTR4
IK
IL3
IL4
IL5
IL9
IL12B
IL13
IRF1
KCNMB1
LCP2
LECT2
LTC4S
SMAD5
MFAP3
MGAT1
MSX2
NDUFA2
NEUROG1
NPY6R
PCDH1
PCDHGC3
PDE6A
PFDN1
PITX1
POU4F3
PPP2CA
PPP2R2B
MAPK9
PROP1
PURA
RARS
RPS14
SGCD
SKP1
SLC6A7
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SNCB
SPARC
SPINK1
SPOCK1
STK10
TAF7
TCF7
ZNF354A
TCOF1
TGFBI
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
NME5
PDLIM4
STC2
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
ATP6V0E1
PTTG1
PDLIM7
CNOT8
HAND1
MED7
MYOT
ADAMTS2
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
CLINT1
PCDHGA8
PCDHA9
MATR3
MAML1
KIAA0141
JAKMIP2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
RAD50
KIF20A
G3BP1
APBB3
TNIP1
GNB2L1
SLU7
RGS14
SEC24A
CPLX2
C5orf4
FAM114A2
BRD8
TCERG1
BTNL3
HNRNPA0
LMAN2
SPINK5
SOX30
KIF3A
MGAT4B
B4GALT7
SYNPO
RNF44
ABLIM3
HMGXB3
TBC1D9B
ARHGAP26
FSTL4
ATP10B
N4BP3
SEPT8
FAF2
WWC1
FBXW11
ACSL6
PHF15
LARP1
HARS2
ZNF346
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
OR4F3
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
UQCRQ
AFF4
PRELID1
IL17B
MAT2B
SLC27A6
MRPL22
PCDHB1
KCNIP1
ZNF354C
ISOC1
RPL26L1
SAR1B
C5orf45
DCTN4
MZB1
PAIP2
CDKL3
PCDH12
FAM13B
FAM53C
REEP2
DDX41
NOP16
LARS
CXXC5
HMP19
UIMC1
RAPGEF6
KDM3B
RAB24
RBM27
NEURL1B
FAM193B
PCDHB18
PCDHB17
TMED9
ZCCHC10
CDHR2
WDR55
ANKHD1
CCDC99
THG1L
TMCO6
GALNT10
NHP2
RBM22
RNF130
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
C5orf15
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
KCTD16
PCDHB16
HMHB1
C5orf54
SIL1
GMCL1P1
ARAP3
RMND5B
PCYOX1L
CCNJL
SH3TC2
PANK3
SAP30L
TXNDC15
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
SLC4A9
SLC25A2
PCDHB19P
PCBD2
PSD2
THOC3
C5orf32
MEGF10
SPINK7
TRIM52
HAVCR2
AGXT2L2
C5orf62
FCHSD1
UNC5A
LYRM7
TRIM41
BOD1
CDKN2AIPNL
COL23A1
TIMD4
ZNF300
MYOZ3
UBTD2
SCGB3A1
SFXN1
FNIP1
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
LEAP2
SCGB3A2
ZNF354B
C5orf47
PPARGC1B
PRRC1
C5orf58
OR2Y1
AFAP1L1
GRPEL2
LSM11
GPR151
ZNF300P1
NUDCD2
UBLCP1
SOWAHA
SHROOM1
C5orf24
C5orf20
SLC36A2
SPINK13
C5orf41
SLC25A48
LOC153469
ZMAT2
BTNL9
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
LOC202181
STK32A
SLC36A1
EIF4E1B
RASGEF1C
LOC257358
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
RELL2
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
OR2V2
ZNF454
C5orf60
CHSY3
LOC340037
TMEM173
LOC340073
LOC340074
ARSI
PFN3
ZNF879
IRGM
FBLL1
CATSPER3
NIPAL4
DND1
C5orf25
FLJ38109
LOC389332
C5orf65
C5orf46
ARHGEF37
C5orf63
SPINK6
ANKHD1-EIF4EBP3
MIR103A1
MIR143
MIR145
MIR146A
MIR218-2
SPINK14
FNDC9
C5orf56
FLJ16171
MIR340
IGIP
TIFAB
LOC553103
CTXN3
SNORD95
SNORD96A
ECSCR
LOC643201
GRXCR2
SPINK9
ZFP62
FLJ33630
CCNI2
CBY3
FAM153C
SNORA74B
MIR585
SNHG4
MIR143HG
LOC728554
LOC729080
AACSP1
LOC729678
OR4F29
VTRNA2-1
MIR874
FAM196B
LOC100132062
LOC100132287
LOC100133331
C5orf52
LOC100268168
MIR1289-2
MIR1229
MIR103B1
MIR3142
MIR3141
MIR4281
MIR3655
MIR3912
MIR3936
MIR3661
LOC100505658
LOC100507387
MIR4633
MIR4634
MIR4461
MIR4460
MIR4638
MIR378E
LOC100859930

Genes in Wide Peak

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

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

Genes
BCL3
ERCC2
KLK2
PPP2R1A
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
A1BG
AP2A1
APOC1
APOC1P1
APOC2
APOC4
APOE
KLK3
BAX
BCAT2
CEACAM1
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CGB
CEACAM8
CKM
AP2S1
CLPTM1
CRX
DBP
DMPK
DMWD
MEGF8
EMP3
ERCC1
ETFB
FCAR
FCGRT
FKBP1AP1
FLT3LG
FOSB
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GIPR
GPR4
GPR32
GRIN2D
ARHGAP35
GYS1
HAS1
FOXA3
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KCNN4
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LHB
LIG1
LIM2
LIPE
BCAM
MYBPC2
NDUFA3
NKG7
CNOT3
NOVA2
NPAS1
NTF4
NUCB1
PEG3
PLAUR
POLD1
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PSG1
PSG2
PSG3
PSG4
PSG5
PSG6
PSG7
PSG9
PSG11
PTGIR
PTPRH
PVR
PVRL2
RELB
RPL18
RPL28
RPS5
RPS9
RPS11
RRAS
RTN2
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPD2
SPIB
AURKC
SULT2B1
SULT2A1
SYT5
TNNI3
TNNT1
TULP2
NR1H2
VASP
XRCC1
ZNF8
ZNF17
ZNF28
MZF1
ZNF45
ZNF221
ZNF222
ZNF132
ZNF134
ZNF135
ZNF137P
ZNF154
ZNF155
ZNF175
ZNF180
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF230
SYMPK
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
PGLYRP1
UBE2M
CYTH2
ZNF235
ZNF264
NCR1
NAPSA
KLK4
ZNF432
DHX34
SAE1
TRIM28
ZNF256
LILRB2
TOMM40
ZNF211
TRAPPC2P1
ZNF234
ZNF274
ZNF460
PPP1R13L
CD3EAP
RUVBL2
LILRB1
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
CLASRP
KPTN
KLK8
PNKP
U2AF2
ATF5
PPP6R1
CARD8
ZC3H4
FBXO46
ETHE1
RPL13A
SYNGR4
LILRA4
PRG1
ZIM2
NUP62
HSPBP1
PPP1R15A
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
UBE2S
SLC6A16
STRN4
CCDC106
EPN1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF581
PTOV1
PPP1R12C
TRPM4
ZNF586
QPCTL
FAM83E
EPS8L1
RASIP1
TMEM160
PIH1D1
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
SMG9
IRGC
CABP5
SPHK2
MEIS3
CEACAM19
SLC17A7
NAT14
CD177
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
USP29
PLEKHA4
MARK4
ZNF71
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
ELSPBP1
LIN7B
HIF3A
ZNF649
ZSCAN18
MGC2752
TSEN34
TRAPPC6A
MBOAT7
FKRP
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF576
ZNF329
TBC1D17
ZNF419
GEMIN7
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
ZNF702P
ZNF606
ZNF614
FUZ
OPA3
RSPH6A
ZNF611
MED25
BCL2L12
TEX101
GRWD1
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
CNFN
SNORD35B
ZNF347
ZNF577
SUV420H2
C19orf48
ZBTB45
ZNF587
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF551
ZNF616
ZNF766
EXOC3L2
ZNF468
ZNF160
CTU1
ZNF835
ZNF765
NLRP12
MYADM
ZNF845
CCDC114
DKFZp434J0226
ACPT
CGB5
CGB7
LRRC4B
LENG9
CGB8
GNG8
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
KIR3DL3
ZNF837
CLDND2
ZNF816
ZNF543
CEACAM20
COX6B2
OSCAR
ZNF813
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
IRGQ
ZNF428
ZFP28
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
PPM1N
KLC3
IGSF23
TMEM190
TMC4
LOC147804
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF296
ZNF579
ZNF114
ZNF525
SPACA4
NLRP7
CADM4
C19orf76
ZNF584
ZSCAN4
NLRP11
TMEM86B
PRR24
ZNF549
NAPSB
IL4I1
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
CXCL17
LOC284344
ZNF575
LYPD5
ZNF283
PPP1R37
NKPD1
TPRX1
MAMSTR
IZUMO1
C19orf63
MGC45922
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
VSTM1
TMEM150B
FAM71E2
VN1R2
VN1R4
NLRP9
MYPOP
NANOS2
ZNF404
ZNF284
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
ZNF530
C19orf51
ZNF233
LILRA5
IGFL1
ZNF773
LOC386758
CEACAM22P
CEACAM16
BLOC1S3
LOC388553
IGFL3
ZNF808
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
LOC390940
ZNF805
ZNF321P
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
LOC646508
SBK2
LOC646862
PSG10P
PHLDB3
SEC1
SNORD23
SNORD88A
SNORD88B
SNORD88C
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
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
SNAR-A14
ERVV-2
LOC100287177
LOC100289650
ZNF587B
MIR1283-2
MIR1323
MIR1283-1
LOC100379224
MIR3191
MIR3190
MIR320E
MIR4324
MIR642B
LOC100505681
LOC100505715
LOC100505812
LOC100506012
LOC100506033
LOC100506068
LOC100507003
ZNF865
ZNF816-ZNF321P
APOC4-APOC2
MIR4754
MIR4752
MIR371B
MIR4749
MIR4750
MIR4531
MIR4751

Genes in Wide Peak

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

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

Genes
BCL6
FOXL2
CBLB
CTNNB1
EIF4A2
ETV5
FANCD2
FHIT
GATA2
LPP
MITF
MLF1
MLH1
MYD88
PIK3CA
PPARG
RAF1
RPN1
SOX2
TFRC
VHL
XPC
BAP1
GMPS
TFG
FOXP1
SETD2
PBRM1
hsa-mir-922
hsa-mir-570
hsa-mir-3137
hsa-mir-944
hsa-mir-28
hsa-mir-1248
hsa-mir-1224
hsa-mir-569
hsa-mir-551b
hsa-mir-720
hsa-mir-1263
hsa-mir-16-2
hsa-mir-1280
hsa-mir-548i-1
hsa-mir-544b
hsa-mir-198
hsa-mir-568
hsa-mir-567
hsa-mir-4273
hsa-mir-1324
hsa-mir-1284
hsa-mir-3136
hsa-mir-4272
hsa-mir-135a-1
hsa-mir-566
hsa-mir-4271
hsa-mir-191
hsa-mir-711
hsa-mir-2115
hsa-mir-1226
hsa-mir-564
hsa-mir-138-1
hsa-mir-26a-1
hsa-mir-128-2
hsa-mir-466
hsa-mir-3135
hsa-mir-563
hsa-mir-3134
hsa-mir-4270
hsa-mir-885
AADAC
ACAA1
ACPP
ACTL6A
ACVR2B
ACY1
ADCY5
ADPRH
AGTR1
AHSG
ALAS1
ALCAM
AMT
APEH
APOD
ARF4
RHOA
ATP1B3
ATP2B2
ATP6V1A
ATR
BCHE
BDH1
BTD
C3orf51
CACNA1D
SLC25A20
CAMP
CASR
CCK
CD80
CD86
ENTPD3
CD47
CDC25A
CISH
AP2M1
CLCN2
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
COL8A1
CP
CPA3
CPB1
CPN2
CPOX
CRYGS
CSTA
CX3CR1
CYP8B1
DAG1
DGKG
DAZL
DLG1
DNASE1L3
DOCK3
DRD3
DUSP7
DVL3
ECT2
CELSR3
EHHADH
EIF4G1
EPHA3
EPHB1
EPHB3
MECOM
FBLN2
FGF12
FLNB
GAP43
GBE1
GHSR
GLB1
GNAI2
GNAT1
GOLGA4
GOLGB1
GP5
GP9
XCR1
GPR15
GPR27
GPX1
GRM2
GSK3B
GTF2E1
GYG1
HCLS1
HGD
HRH1
HRG
HES1
HTR1F
HYAL1
IL1RAP
IL12A
IMPDH2
IRAK2
ITGA9
ITGB5
ITIH1
ITIH3
ITIH4
KNG1
KPNA1
KPNA4
LAMB2
RPSA
LSAMP
LTF
TM4SF1
MAP4
MBNL1
MCM2
MFI2
MME
MOBP
CD200
MST1
MST1R
MUC4
MYL3
MYLK
NCK1
NDUFB4
NDUFB5
NKTR
OGG1
OPA1
CLDN11
P2RY1
PAK2
CNTN3
PCCB
PCYT1A
PDHB
PFKFB4
PFN2
SERPINI1
SERPINI2
PIK3CB
PLCD1
PLD1
PLOD2
PLS1
PLSCR1
PLXNA1
PLXNB1
POLR2H
POU1F1
PPP1R2
PPP2R3A
PRKAR2A
PRKCD
PRKCI
PROS1
MASP1
PSMD2
PTH1R
PTPRG
PTX3
QARS
RAB5A
RAP2B
RARB
RARRES1
RASA2
RBP1
RBP2
RFC4
RHO
SNORA63
SNORA62
ROBO1
ROBO2
RPL15
RPL24
RPL29
RPL32
RPL35A
RYK
SATB1
ATXN7
SCN5A
SCN10A
SEC13
SEMA3F
TRA2B
SHOX2
SI
SIAH2
ST6GAL1
SKIL
SLC2A2
SLC6A1
SLC6A6
SLC6A11
SLC15A2
SLCO2A1
HLTF
SMARCC1
SSR3
SST
STAC
NEK4
SYN2
TCTA
TDGF1
TERC
TF
TFDP2
TGM4
TGFBR2
THPO
THRB
TIMP4
TKT
SEC62
TM4SF4
TMF1
CLEC3B
TNNC1
TOP2B
NR2C2
TRH
TRPC1
UBA7
UBE2E1
UBE2E2
UBP1
UPK1B
UMPS
USP4
UQCRC1
CLRN1
VIPR1
WNT5A
WNT7A
ZIC1
CNBP
ZNF35
ZNF80
ZNF148
BRPF1
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
RAB7A
KCNAB1
FXR1
COLQ
ACOX2
EOMES
HYAL3
SOX14
BFSP2
CAMK1
CGGBP1
RUVBL1
CADPS
TP63
CHRD
HYAL2
B4GALT4
B3GALNT1
SNX4
TNFSF10
SUCLG2
HESX1
KAT2B
NR1I2
EIF2B5
BSN
MBD4
H1FX
USP13
LIMD1
KALRN
CCRL2
UBA3
RPL14
CLDN1
SEC22C
RRP9
MAP3K13
SLC33A1
LRRFIP2
MAGI1
CACNA2D2
COPB2
ADIPOQ
SLC22A14
SLC22A13
CHST2
SH3BP5
SLC4A7
STXBP5L
RNF7
GUCA1C
IQCB1
DZIP3
VGLL4
KIAA0226
ECE2
VPRBP
TBC1D5
TATDN2
IP6K1
TSC22D2
EPM2AIP1
PSMD6
TOMM70A
TRANK1
IQSEC1
P2RY14
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
PARP3
SMC4
ABCC5
COX17
ARPC4
ZNF197
RBM6
RBM5
TNK2
ALG3
NME6
CTDSPL
CD96
KCNMB2
STAG1
EIF1B
TRAIP
ST3GAL6
ARIH2
TADA3
CRTAP
ATG7
ARL6IP5
NPRL2
IGF2BP2
CXCR6
CSPG5
CLDN16
POLQ
ARPP21
CCR9
ALDH1L1
USP19
PDIA5
SLC38A3
CYB561D2
TMEM115
TOPBP1
RPP14
HHLA2
FSTL1
FAM107A
WDR6
RASSF1
NISCH
MRPL3
PDCD10
FILIP1L
TREX1
SCN11A
TUSC2
RNF13
MGLL
TWF2
MRAS
COPG
SLITRK3
NLGN1
TRAK1
DHX30
SACM1L
NCBP2
SCAP
LAMB2P1
MYH15
PLCH1
EXOSC7
TMCC1
PDZRN3
TNIK
CAND2
MCF2L2
CLASP2
PLXND1
RAD54L2
FRMD4B
STAB1
GPD1L
RFTN1
ATP11B
NBEAL2
NUP210
PLCL2
ANKRD28
FAM208A
KLHL18
DNAJC13
U2SURP
VPS8
LARS2
RYBP
C3orf27
CAPN7
ACAP2
MKRN2
NAT6
FBXL2
ANAPC13
ARMC8
ABHD14A
C3orf17
POC1A
ABI3BP
CNOT10
TMEM158
NDUFAF3
MYRIP
PTPN23
WWTR1
PVRL3
TIPARP
CHMP2B
DNAH1
HIGD1A
LRIG1
SUSD5
UBXN7
ERC2
APPL1
HACL1
ARHGEF26
ZBTB20
TTLL3
OR5K1
OR5H1
GNL3
FAM162A
PCOLCE2
SEC22A
GPR160
FETUB
NPHP3
ATP2C1
LAMP3
KCNMB3
ZBTB11
MORC1
SERP1
LSM3
RBMS3
GOLIM4
NKIRAS1
SPCS1
ACAD9
ASTE1
KLF15
GTPBP8
TAGLN3
PRSS50
RBM15B
GPR171
GMPPB
SEC61A1
SCHIP1
PIK3R4
PODXL2
ARHGEF3
TRAT1
VILL
IMPG2
NMD3
ABHD5
COMMD2
DYNC1LI1
A4GNT
C3orf18
DBR1
SS18L2
ZNF639
CLDN18
C3orf19
SHISA5
TIMMDC1
ZDHHC3
RSRC1
ZMYND10
PLA1A
TEX264
CCDC72
ZNF589
HEMK1
AMOTL2
IP6K2
SFMBT1
NCKIPSD
PHF7
CCRL1
PEX5L
RAB6B
SELT
FBXO40
DNAJB11
GHRL
P2RY13
IL20RB
GPR87
TLR9
DCUN1D1
SEMA5B
XRN1
WDR5B
LZTFL1
PARP14
P4HTM
SLC6A20
IL17RD
GRAMD1C
ROPN1
KLHL24
SIDT1
C3orf75
SNRK
QRICH1
PXK
CMTM6
RG9MTD1
SLC41A3
PIGX
SLC25A38
ULK4
OXSM
SLC35A5
TMEM45A
FEZF2
IFT57
EBLN2
ANO10
DALRD3
SHQ1
MSL2
TBCCD1
FAIM
SLC25A36
DPPA4
LEPREL1
TMEM39A
ZNF654
TMEM40
ABCF3
LSG1
ABHD10
CHDH
PARL
IL17RB
CDV3
MFN1
YEATS2
IFT122
NGLY1
TBC1D23
WDR52
CACNA2D3
DCP1A
GLT8D1
TMEM111
EAF2
BRK1
ZNF167
MYNN
LMOD3
EIF5A2
CLDND1
MUC13
SUCNR1
SEMA3G
MCCC1
LXN
C3orf37
MRPS22
NIT2
POGLUT1
BBX
KIF15
ADAMTS9
CCNL1
PLSCR2
PCBP4
PLSCR4
PCNP
HRASLS
MRPL47
SENP7
ABHD6
LRTM1
C3orf14
KIAA1143
ISY1
HHATL
HEG1
KIAA1257
ARHGAP31
NCEH1
IFT80
KIAA1407
WDR48
KIAA1524
SLC7A14
SRPRB
SELK
SENP2
GNB4
BPESC1
PROK2
EEFSEC
RNF123
NSUN3
CIDEC
CLSTN2
POPDC2
RTP4
MAGEF1
ZFYVE20
KIF9
NFKBIZ
AZI2
ZMAT3
ATG3
MRPS25
CSRNP1
GORASP1
MFSD1
CCDC14
FNDC3B
P2RY12
CDCP1
CCDC71
NT5DC2
SLC26A6
TMEM108
CRELD1
CAMKV
TMEM43
OR5H6
OR5H2
ZXDC
ZBED2
LRRC2
FYCO1
ATP13A3
CEP97
HSPBAP1
C3orf52
VEPH1
QTRTD1
CCDC51
TBL1XR1
ZBBX
ZNF385D
LRRC31
CCDC48
NEK11
UBA5
HDAC11
MAP6D1
PHC3
C3orf36
ARL14
THOC7
NAA50
PIGZ
CEP63
CEP70
ABTB1
WDR82
TMEM22
TSEN2
GRIP2
OR5AC2
RTP3
PARP9
ESYT3
SPATA16
EIF2A
B3GNT5
C3orf20
ID2B
ARL6
ZIC4
ATRIP
ACAD11
IQCG
ATP13A4
FYTTD1
NICN1
CHCHD6
MON1A
C3orf26
HPS3
ARPM1
JAGN1
KBTBD8
SLC12A8
GHRLOS2
RETNLB
CCDC54
MGC2889
IL17RC
ABHD14B
LRCH3
MINA
GPR128
C3orf39
DIRC2
CEP19
EAF1
DCLK3
GFM1
LMLN
KLHL6
C3orf15
PHLDB2
VWA5B2
UCN2
LOC90246
C3orf25
TMEM41A
ZNF502
BOC
FAM55C
RFT1
OXNAD1
SPSB4
ACPL2
ZBTB47
TMEM44
EGFEM1P
ACTR8
CAMK2N2
CMTM7
TXNRD3
OSBPL10
OSBPL11
SLC25A26
ZNF501
C3orf24
LRRC58
LRRC3B
TM4SF19
TM4SF18
RPL39L
MED12L
CLRN1-AS1
GALNTL2
GPR62
CPNE4
CCDC58
KCNH8
DNAJC19
OTOL1
FAM3D
ZPLD1
LYZL4
KBTBD5
TRIM71
FAM131A
CD200R1
CHCHD4
ZDHHC19
DCBLD2
LRRC15
FAM43A
TPRA1
TMEM42
UROC1
FAM194A
NUDT16
COL6A6
GRK7
FAM172BP
TMEM207
METTL6
TAMM41
IL17RE
RTP1
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
RPL32P3
H1FOO
PISRT1
ASB14
TTC14
DTX3L
FAM19A4
SGOL1
PP2D1
EFHB
LOC151658
PPM1L
WDR49
LRRC34
CPNE9
DPPA2
CCDC80
BTLA
CCDC12
MB21D2
PPP4R2
XXYLT1
ROPN1B
LOC152024
C3orf22
C3orf55
ZCWPW2
CMC1
NEK10
C3orf79
CCDC50
PYDC2
SPICE1
CMTM8
NUDT16P1
CCDC13
LOC152217
LOC152225
FGD5
CIDECP
IGSF11
C3orf30
PARP15
SPTSSB
DNAJB8
GPR156
XIRP1
RNF168
CHST13
PRICKLE2
KBTBD12
DHX36
HTR3C
DZIP1L
TTC21A
ALG1L
C3orf67
KCTD6
LIPH
ARL13B
DHFRL1
HTR3D
RPL22L1
OSTalpha
FBXO45
KLHDC8B
MUC20
GABRR3
PTPLB
STT3B
LOC201617
DNAH12
PDE12
FAM116A
TIGIT
LOC201651
C3orf58
SENP5
KIAA2018
LOC220729
ZBTB38
CADM2
LOC253573
ZNF620
NAALADL2
ZDHHC23
LOC255025
NUP210P1
TCTEX1D2
C3orf43
SDHAP1
COL6A5
GK5
PLCXD2
GCET2
UTS2D
ALS2CL
TMIE
LSAMP-AS3
SLC9A9
C3orf64
LOC285205
EPHA6
DNAJB8-AS1
FBXW12
C3orf38
HTR3E
ENTPD3-AS1
ZNF619
ZNF621
RABL3
IGSF10
C3orf33
LOC285326
CCDC66
SLC9A10
C3orf23
ZNF660
FLJ39534
LOC285359
RPUSD3
PRRT3
LOC285370
LOC285375
DPH3
C3orf70
TPRG1
LOC285401
ILDR1
TRIM59
TRIM42
EIF4E3
RAB43
CCDC39
CCDC36
KY
LOC339862
LOC339874
C3orf35
LOC339894
GADL1
PRSS42
LOC339926
LPP-AS2
H1FX-AS1
LOC344595
LRRIQ4
SAMD7
AADACL2
GPR149
ZNF860
TMPRSS7
CD200R1L
PAQR9
COL6A4P1
LOC344887
RTP2
OSTN
ATP13A5
SOX2-OT
NME9
WDR53
LNP1
CCDC37
NPHP3-AS1
TPRXL
ANKRD18DP
NMNAT3
ZNF445
SPATA12
C3orf77
C3orf62
TMEM110
LRRC33
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VGLL3
PRR23B
PRR23C
PLSCR5
ANKUB1
LEKR1
TMEM212
VENTXP7
LOC401052
IQCF3
LOC401074
FLJ22763
FLJ25363
C3orf72
LOC401093
C3orf80
FLJ46066
FLJ42393
FLJ34208
LOC401109
OR5K2
OR5H14
OR5H15
OR5K3
OR5K4
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR15B
MIR16-2
MIR191
MIR198
MIR26A1
FAM19A1
STX19
FLJ33065
TMEM89
IQCF6
C3orf78
LOC440970
MIR425
ARGFX
SNORA6
SNORA7A
SNORD2
SNORA4
TMPPE
TMEM30C
LOC644714
ALG1L2
LOC644990
LOC645206
TXNRD3NB
TMEM14E
LOC646168
COL6A4P2
SPINK8
C3orf71
LOC646498
C3orf65
LOC646903
PA2G4P4
LOC647107
GMNC
LOC647323
FLJ20518
LOC653712
IQCJ
SCARNA7
LINC00488
SNORA7B
SNORA58
SNORA81
SNORD19
FAM86DP
SNORD66
SNORD69
MIR548A2
MIR548A3
MIR551B
MIR563
MIR564
MIR567
MIR568
MIR569
MIR570
GXYLT2
SDHAP2
FAM157A
FAM198A
CCR2
FAM86HP
PRR23A
LOC730091
ESRG
LOC100009676
SNORD19B
LOC100125556
MIR922
MIR885
MIR944
GHRLOS
LOC100128023
WWTR1-AS1
LOC100128164
C3orf74
LOC100128640
NRADDP
LOC100129480
LOC100129550
ZBTB20-AS1
LOC100131551
LOC100131635
ZNF717
LOC100132146
LOC100132526
BSN-AS2
SNAR-I
MIR1224
TIPARP-AS1
PRSS46
LOC100287879
FRG2C
LOC100289361
MIR1284
MIR1248
MIR1280
MIR548I1
MIR1324
MIR1226
LOC100302640
MIR548H2
MIR711
MIR548G
MIR3136
MIR4270
MIR4272
MIR4271
MIR4273
LOC100498859
MIR3919
MIR3921
MIR3938
MIR3714
IQCJ-SCHIP1
FGD5-AS1
LOC100505687
LOC100505696
KRBOX1
PVRL3-AS1
IGSF11-AS1
MYLK-AS1
IQCF4
LOC100506994
LOC100507032
MFI2-AS1
LOC100507062
LOC100507086
ADAMTS9-AS2
LOC100507389
LOC100507391
ARHGEF26-AS1
LOC100507537
ARPC4-TTLL3
ABHD14A-ACY1
TMEM110-MUSTN1
NPHP3-ACAD11
ISY1-RAB43
TM4SF19-TCTEX1D2
MIR4793
MIR4787
MIR4795
MIR4796
MIR4797
MIR4788
MIR4791
MIR548AC
MIR4444-1
MIR4789
MIR4443
MIR4792
MIR4446
MIR4442
LOC100652759
LUST

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q13.2.

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

Genes
BUB1B
PML
TCF12
FLJ27352
C15orf55
hsa-mir-549
hsa-mir-184
hsa-mir-4313
hsa-mir-631
hsa-mir-630
hsa-mir-629
hsa-mir-4312
hsa-mir-4311
hsa-mir-1272
hsa-mir-422a
hsa-mir-190
hsa-mir-2116
hsa-mir-628
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
ACTC1
ADAM10
ANXA2
APBA2
AQP9
B2M
BBS4
BCL2A1
NBEAP1
BNIP2
CA12
CAPN3
CHRM5
CHRNA3
CHRNA5
CHRNA7
CHRNB4
CKMT1B
CLK3
CRABP1
CSK
CSPG4
CTSH
CYP1A1
CYP1A2
CYP11A1
CYP19A1
DUT
EPB42
ETFA
FAH
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
GTF2A2
HDC
HEXA
ONECUT1
IDH3A
IPW
IREB2
ISLR
ITPKA
IVD
LIPC
LOXL1
LTK
SMAD3
SMAD6
MAN2C1
MAP1A
MEIS2
MFAP1
TRPM1
MPI
MYO1E
MYO5A
MYO9A
NDN
NEDD4
NEO1
OAZ2
OCA2
PKM2
PLCB2
PPIB
MAPK6
MAP2K1
MAP2K5
PSMA4
PTPN9
RAB27A
RAD51
RASGRF1
RCN2
RORA
RPL4
RPLP1
RYR3
SCG5
SLC12A1
SNRPN
SNX1
SORD
SPINT1
SRP14
THBS1
TJP1
TLE3
TP53BP1
TPM1
TYRO3
TYRO3P
UBE3A
MKRN3
SLC30A4
PAR5
ANP32A
SEMA7A
CILP
PIAS1
EIF3J
JMJD7-PLA2G4B
RAB11A
SNAP23
ALDH1A2
HERC2
HERC1
SNURF
PSTPIP1
USP8
CCNB2
SLC28A2
SLC24A1
CCPG1
GCNT3
COPS2
TRIP4
TGM5
COX5A
STOML1
PIGB
KIF23
IGDCC3
PPIP5K1
AQR
SECISBP2L
KIAA0101
ARHGAP11A
LCMT2
ARNT2
USP3
SLC12A6
NR2E3
BCL2L10
HCN4
SCAMP2
SNUPN
PDCD7
TSPAN3
FEM1B
RASGRP1
SERF2
DENND4A
SNAPC5
HMG20A
CORO2B
CIB2
MTHFS
ARID3B
GNB5
ARPP19
CLPX
MORF4L1
SLC27A2
ADAMTS7
GPR176
CHP
OIP5
ITGA11
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
ZNF609
TBC1D2B
RTF1
CYFIP1
ACSBG1
KIAA1024
MGA
DMXL2
VPS39
FAM189A1
TMED3
AP4E1
CCNDBP1
DAPK2
EID1
C15orf2
C15orf63
ARIH1
SIN3A
TMEM87A
ULK3
RPAP1
GLCE
DKFZP434L187
PYGO1
PLDN
FBXO22
GREM1
NPTN
FOXB1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
SCAPER
DUOX2
MYEF2
RPS27L
NDUFAF1
RSL24D1
NUSAP1
TMEM85
RASL12
SPG21
SPTBN5
PTPLAD1
CTDSPL2
KLF13
RAB8B
DUOX1
CSNK1G1
ZFAND6
MAGEL2
DLL4
INO80
FAM63B
RNF111
ZNF280D
TRPM7
VPS13C
LRRC49
PAQR5
PPP1R14D
DPP8
MTMR10
RPP25
COMMD4
PARP16
TIPIN
CLN6
ZNF770
ZWILCH
FLJ10038
UACA
HAUS2
FAM82A2
DNAJC17
IMP3
LARP6
MNS1
DNAJA4
NOP10
GOLGA6B
MYO5C
NDNL2
FAM214A
C15orf24
C15orf39
THAP10
PAK6
PARP6
DTWD1
CASC5
AVEN
C15orf17
ATP10A
KIAA1199
GJD2
STARD9
ISLR2
VPS18
IGDCC4
SQRDL
FAM108C1
PPCDC
CELF6
STRA6
ZFP106
IQCH
ISL2
RFX7
SPATA5L1
CHAC1
NOX5
NEIL1
NARG2
AAGAB
LMAN1L
C15orf29
SLTM
PEAK1
SNX22
THSD4
ATP8B4
WDR76
TMEM62
SEMA6D
ANP32A-IT1
C15orf34
PIF1
CCDC33
EDC3
SPG11
ELL3
PLEKHO2
WDR61
CD276
POLR2M
C15orf44
NIPA2
C15orf5
ADPGK
APH1B
TLN2
FAM96A
C15orf48
MEGF11
C15orf41
SPPL2A
LINGO1
ZFYVE19
CGNL1
FRMD5
UBL7
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
LOC91450
CALML4
LDHAL6B
UBE2Q2
CHST14
CASC4
LACTB
TUBGCP5
DIS3L
TGM7
CATSPER2
LEO1
SENP8
MTFMT
OSTBETA
HIGD2B
C15orf27
NIPA1
AGPHD1
PLA2G4E
TRIM69
PAR1
C15orf43
LOC145663
C2CD4A
FAM81A
GCOM1
LOC145783
LOC145837
LOC145845
C15orf61
TMCO5A
NRG4
ZSCAN29
TTBK2
CDAN1
STRC
TBC1D21
DYX1C1
CSNK1A1P1
OTUD7A
SPRED1
ODF3L1
PGBD4
ADAL
EXD1
FSIP1
RHOV
SCAMP5
C15orf33
CT62
GRAMD2
MGC15885
LCTL
UBR1
PATL2
SPESP1
LOC253044
LPCAT4
PLA2G4F
LRRC57
LYSMD2
WDR72
SNX33
HMGN2P46
SLC24A5
PRTG
LOC283663
LINC00277
C15orf60
LOC283683
C15orf37
LOC283688
OR4N4
LOC283710
LOC283731
FAM98B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
FBXL22
SNORD108
SNORD109A
SNORD109B
SNORD115-1
TMEM202
WHAMMP3
POTEB
GLDN
GOLGA6A
FMN1
SNORD64
PAR4
PAR-SN
RBPMS2
ANKDD1A
LOC348120
MRPL42P5
USP50
TEX9
C15orf52
TNFAIP8L3
C2CD4B
C15orf59
GOLGA8E
OR4M2
OR4N3P
KBTBD13
UBAP1L
SKOR1
ANKRD34C
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
ST20
DUOXA2
MIR184
MIR190A
MIR211
C15orf50
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
LOC440288
LOC503519
CKMT1A
CPLX3
SNORD16
SNORD18A
SNORD18B
SNORD18C
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
LOC645752
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
SH2D7
LOC646938
LOC653061
LOC653075
GOLGA6C
GOLGA6D
HSP90AB4P
SCARNA14
FBXO22-AS1
MIR549
MIR626
MIR627
MIR628
MIR629
MIR630
MIR631
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
OIP5-AS1
LOC729739
GOLGA8C
LOC729911
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
MIR147B
DNM1P35
LOC100128714
LOC100129387
LOC100130855
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
LOC100132724
GOLGA8DP
JMJD7
PLA2G4B
LOC100287559
LOC100287616
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1272
MIR1266
MIR1282
LOC100306975
MIR548H4
MIR2116
MIR1233-2
MIR4311
MIR4312
MIR4310
MIR4313
MIR3942
LOC100505648
LOC100506686
LOC100507466
ST20-MTHFS
SERF2-C15ORF63
DYX1C1-CCPG1
MIR4513
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4716
MIR4713
MIR4511
MIR4509-3
MIR4712
MIR4715
TMCO5B
MYZAP

Arm-level results

Table 3. Get Full Table Arm-level significance table - 12 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.18 | 0.146 | 0.987 | 0.28 | 1.46 | 0.24
1q | 1955 | 0.14 | -0.457 | 0.987 | 0.27 | 1.29 | 0.282
2p | 924 | 0.13 | -0.752 | 0.987 | 0.23 | 0.499 | 0.597
2q | 1556 | 0.04 | -1.77 | 0.987 | 0.18 | -0.0274 | 0.73
3p | 1062 | 0.05 | -1.73 | 0.987 | 0.25 | 0.814 | 0.479
3q | 1139 | 0.04 | -1.78 | 0.987 | 0.21 | 0.352 | 0.615
4p | 489 | 0.08 | -1.57 | 0.987 | 0.11 | -1.16 | 0.899
4q | 1049 | 0.08 | -1.47 | 0.987 | 0.11 | -1.04 | 0.897
5p | 270 | 0.16 | -0.55 | 0.987 | 0.16 | -0.55 | 0.826
5q | 1427 | 0.17 | -0.206 | 0.987 | 0.20 | 0.221 | 0.655
6p | 1173 | 0.26 | 0.9 | 0.987 | 0.26 | 0.9 | 0.46
6q | 839 | 0.27 | 0.973 | 0.987 | 0.14 | -0.682 | 0.826
7p | 641 | 0.27 | 0.919 | 0.987 | 0.14 | -0.72 | 0.826
7q | 1277 | 0.24 | 0.698 | 0.987 | 0.17 | -0.146 | 0.769
8p | 580 | 0.21 | 0.12 | 0.987 | 0.21 | 0.12 | 0.67
8q | 859 | 0.15 | -0.596 | 0.987 | 0.08 | -1.44 | 0.924
9p | 422 | 0.20 | -0.0168 | 0.987 | 0.36 | 1.98 | 0.0998
9q | 1113 | 0.23 | 0.462 | 0.987 | 0.29 | 1.29 | 0.282
10p | 409 | 0.00 | -2.19 | 0.987 | 0.34 | 1.92 | 0.0998
10q | 1268 | 0.00 | -2.03 | 0.987 | 0.38 | 2.68 | 0.0215
11p | 862 | 0.06 | -1.48 | 0.987 | 0.39 | 2.67 | 0.0215
11q | 1515 | 0.05 | -1.52 | 0.987 | 0.32 | 1.92 | 0.0998
12p | 575 | 0.04 | -1.93 | 0.987 | 0.18 | -0.267 | 0.807
12q | 1447 | 0.04 | -1.85 | 0.987 | 0.14 | -0.544 | 0.826
13q | 654 | 0.00 | -1.92 | 0.987 | 0.48 | 3.86 | 0.00223
14q | 1341 | 0.18 | -0.0857 | 0.987 | 0.46 | 3.64 | 0.00272
15q | 1355 | 0.09 | -1.13 | 0.987 | 0.26 | 1 | 0.42
16p | 872 | 0.21 | 0.188 | 0.987 | 0.21 | 0.188 | 0.655
16q | 702 | 0.17 | -0.317 | 0.987 | 0.42 | 2.91 | 0.0144
17p | 683 | 0.09 | -1.32 | 0.987 | 0.22 | 0.334 | 0.615
17q | 1592 | 0.12 | -0.78 | 0.987 | 0.15 | -0.346 | 0.82
18p | 143 | 0.14 | -0.814 | 0.987 | 0.27 | 0.788 | 0.479
18q | 446 | 0.17 | -0.325 | 0.987 | 0.24 | 0.486 | 0.597
19p | 995 | 0.12 | -0.902 | 0.987 | 0.15 | -0.481 | 0.826
19q | 1709 | 0.00 | -2.23 | 0.987 | 0.21 | 0.411 | 0.615
20p | 355 | 0.22 | 0.175 | 0.987 | 0.25 | 0.576 | 0.595
20q | 753 | 0.27 | 0.949 | 0.987 | 0.14 | -0.698 | 0.826
21q | 509 | 0.20 | 0.00107 | 0.987 | 0.36 | 2 | 0.0998
22q | 921 | 0.12 | -0.781 | 0.987 | 0.44 | 3.32 | 0.00454
Xq | 1312 | 0.06 | -1.34 | 0.987 | 0.43 | 3.32 | 0.00454

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/SARC-TP/2172002/2.GDAC_MergeDataFiles.Finished/SARC-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 4. Get Full Table First 10 out of 29 Input Tumor Samples.

Tumor Sample Names
TCGA-DX-A2IZ-01A-11D-A21P-01
TCGA-DX-A2J0-01A-11D-A21P-01
TCGA-DX-A2J1-01A-11D-A21P-01
TCGA-DX-A2J4-01A-32D-A21P-01
TCGA-DX-A3LS-01A-11D-A21P-01
TCGA-DX-A3LT-01A-12D-A21P-01
TCGA-DX-A3LU-01A-11D-A21P-01
TCGA-DX-A3LW-01A-21D-A21P-01
TCGA-DX-A3M1-01A-11D-A227-01
TCGA-DX-A3M2-01A-21D-A227-01

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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