Copy number analysis (GISTIC2)
Sarcoma (Primary solid tumor)
23 May 2013 | analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C1RN35Z6
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1RN35Z6
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 2.0.17a (Firehose task version: 0.0.8).

Summary

There were 52 tumor samples used in this analysis: 10 significant arm-level results, 13 significant focal amplifications, and 28 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 - 13 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
--- | --- | --- | --- | ---
12q15 | 7.9143e-33 | 7.9143e-33 | chr12:69199208-69244387 | 1
1q24.3 | 8.5006e-06 | 8.5006e-06 | chr1:171483980-172409462 | 11
5p15.33 | 0.0026403 | 0.0026403 | chr5:1019815-1300024 | 6
6p21.1 | 0.012902 | 0.012902 | chr6:41698135-42692619 | 17
6q25.1 | 0.022455 | 0.022455 | chr6:149996721-150644383 | 13
17p12 | 0.034148 | 0.034148 | chr17:10231418-17646775 | 73
19p13.2 | 0.037749 | 0.037749 | chr19:6882410-7309686 | 9
11q22.2 | 0.067719 | 0.067719 | chr11:101789694-102797954 | 15
Xq21.1 | 0.10829 | 0.10829 | chrX:76793273-89210865 | 36
12p13.32 | 0.12274 | 0.12274 | chr12:4747451-5351735 | 6
4p15.2 | 0.1319 | 0.1319 | chr4:16912788-26191365 | 34
1p32.2 | 0.14924 | 0.14924 | chr1:58400165-61214126 | 12
7p15.3 | 0.24529 | 0.24529 | chr7:18906542-36312081 | 136

Genes in Wide Peak

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

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

Genes
MDM2

Genes in Wide Peak

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

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

Genes
hsa-mir-199a-2
MYOC
VAMP4
PRRC2C
DNM3
METTL13
C1orf105
MIR199A2
MIR214
MIR3120
DNM3OS

Genes in Wide Peak

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

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

Genes
TERT
SLC12A7
NKD2
SLC6A19
SLC6A18
MIR4635

Genes in Wide Peak

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

Table S4. 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 6q25.1.

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

Genes
PCMT1
LATS1
ULBP3
ULBP2
ULBP1
PPP1R14C
LRP11
RAET1E
RAET1L
NUP43
RAET1G
RAET1K
LOC100652739

Genes in Wide Peak

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

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

Genes
MAP2K4
hsa-mir-1288
hsa-mir-548h-3
hsa-mir-744
ADORA2B
COX10
DNAH9
MEIS3P1
MYH1
MYH2
MYH3
MYH4
MYH8
PMP22
SCO1
UBB
ZNF18
COPS3
MYH13
PIGL
NCOR1
CCDC144A
ARHGAP44
HS3ST3B1
HS3ST3A1
PEMT
TRIM16
RAI1
MPRIP
TNFRSF13B
SNORD49A
TRPV2
RASD1
TTC19
MED9
NT5M
C17orf48
ZNF286A
ZNF287
ZNF624
ELAC2
TEKT3
MGC12916
MYOCD
CDRT7
CDRT15P1
C17orf76-AS1
ZSWIM7
SMCR9
CDRT15
USP32P1
FAM18B2
CENPV
FLCN
PLD6
FLJ34690
CDRT4
TBC1D26
CDRT1
TMEM220
SHISA6
FAM211A
KRT16P2
PIRT
CDRT15P2
SNORD49B
SNORD65
MIR744
FAM106CP
LOC100289255
MIR1288
FAM18B2-CDRT4
MIR4731

Genes in Wide Peak

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

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

Genes
EMR1
INSR
ZNF557
MBD3L2
MBD3L5
EMR4P
FLJ25758
MBD3L4
MBD3L3

Genes in Wide Peak

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

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

Genes
BIRC3
BIRC2
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP20
YAP1
KIAA1377
MMP27
C11orf70
TMEM123
LOC100288077

Genes in Wide Peak

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

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

Genes
ATRX
hsa-mir-361
hsa-mir-548i-4
hsa-mir-4328
ATP7A
CHM
COX7B
CYLC1
LPAR4
PGK1
POU3F4
SH3BGRL
ZNF711
ITM2A
CYSLTR1
RPS6KA6
P2RY10
TBX22
TAF9B
CPXCR1
KLHL4
HMGN5
POF1B
MAGT1
GPR174
TGIF2LX
DACH2
APOOL
HDX
FAM46D
ZCCHC5
BRWD3
SATL1
PGAM4
UBE2DNL
MIR4328

Genes in Wide Peak

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

Table S10. 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 4p15.2.

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

Genes
hsa-mir-573
hsa-mir-218-1
DHX15
QDPR
SOD3
SLIT2
SLC34A2
PPARGC1A
SEL1L3
FAM184B
ZCCHC4
ANAPC4
LAP3
SEPSECS
DCAF16
LGI2
PI4K2B
GBA3
NCAPG
MED28
KCNIP4
CCDC149
PACRGL
GPR125
LCORL
LOC285540
KCNIP4-IT1
C4orf52
MIR218-1
CLRN2
MIR573
SLIT2-IT1
LOC100505912
MIR548AJ2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p32.2.

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

Genes
JUN
CYP2J2
DAB1
TACSTD2
HOOK1
FGGY
MYSM1
OMA1
C1orf87
HSD52
LOC100131060
MIR4711

Genes in Wide Peak

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

Table S13. 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

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

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
9p21.3 | 2.6146e-07 | 2.6146e-07 | chr9:21865498-22448737 | 4
13q14.2 | 3.1632e-06 | 5.9465e-06 | chr13:48833767-49798173 | 6
Xq21.1 | 8.1532e-06 | 9.2973e-06 | chrX:76225229-77102528 | 3
2q37.3 | 9.3478e-06 | 9.3478e-06 | chr2:242162274-243199373 | 17
11p15.5 | 0.0021711 | 0.0022181 | chr11:1-929549 | 50
17p13.1 | 0.0024425 | 0.0023685 | chr17:7613709-7744654 | 2
11q22.3 | 0.0015959 | 0.0084498 | chr11:92082777-135006516 | 362
21q22.3 | 0.0097023 | 0.00931 | chr21:47427840-47609222 | 3
17q25.3 | 0.010389 | 0.0099594 | chr17:80443432-80617015 | 2
4q35.1 | 0.01357 | 0.01357 | chr4:156678656-191154276 | 143
1q44 | 0.025279 | 0.025279 | chr1:204795036-249250621 | 375
9q34.3 | 0.028833 | 0.027976 | chr9:131934548-141213431 | 201
19q13.33 | 0.036061 | 0.034754 | chr19:44382732-50837901 | 280
12p12.3 | 0.038364 | 0.039793 | chr12:1-39838485 | 340
3q25.1 | 0.040986 | 0.041197 | chr3:134970850-163894013 | 157
10p15.3 | 0.041844 | 0.041197 | chr10:1-857150 | 4
Xq28 | 0.036623 | 0.041197 | chrX:147107975-149615811 | 15
8p23.2 | 0.055609 | 0.054405 | chr8:1-9414641 | 73
1p32.3 | 0.038689 | 0.062914 | chr1:50879767-51569162 | 3
19p13.3 | 0.06901 | 0.069092 | chr19:1-3187429 | 120
14q24.1 | 0.10601 | 0.10601 | chr14:1-102523336 | 722
1p36.32 | 0.048283 | 0.10772 | chr1:1-29140747 | 483
3p21.31 | 0.18489 | 0.18652 | chr3:23972868-87328364 | 451
6q15 | 0.1925 | 0.18957 | chr6:47864832-171115067 | 575
7q36.3 | 0.18957 | 0.18957 | chr7:113516404-159138663 | 357
11q25 | 0.00076181 | 0.20479 | chr11:68224043-135006516 | 542
13q34 | 0.09131 | 0.22014 | chr13:1-115169878 | 414
5q23.3 | 0.22497 | 0.22497 | chr5:102461774-180915260 | 612

Genes in Wide Peak

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

Table S14. 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 13q14.2.

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

Genes
RB1
RCBTB2
MLNR
LPAR6
FNDC3A
CYSLTR2

Genes in Wide Peak

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

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

Genes
ATRX
hsa-mir-325
FGF16

Genes in Wide Peak

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

Table S17. 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 11p15.5.

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

Genes
HRAS
hsa-mir-210
CD151
DRD4
IRF7
POLR2L
PSMD13
RNH1
RPLP2
SCT
TALDO1
TSPAN4
RASSF7
IFITM1
IFITM3
DEAF1
IFITM2
PKP3
SIRT3
BET1L
CEND1
CDHR5
PIDD
PNPLA2
PHRF1
SIGIRR
RIC8A
EPS8L2
CHID1
SLC25A22
ATHL1
PTDSS2
ODF3
LRRC56
LOC143666
SCGB1C1
NLRP6
NS3BP
C11orf35
EFCAB4A
TMEM80
ANO9
B4GALNT4
PDDC1
IFITM5
MIR210
SNORA52
LOC653486
LOC100133161
MIR210HG

Genes in Wide Peak

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

Table S19. 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 11q22.3.

Table S20. 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
PCSK7
ARHGEF12
MAML2
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
hsa-mir-1260b
hsa-mir-548l
hsa-mir-1304
ACAT1
ACRV1
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
FUT4
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
MRE11A
MTNR1B
NCAM1
NFRKB
NNMT
NPAT
NRGN
OPCML
PGR
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
THY1
TRPC6
UPK2
ZBTB16
ZNF202
CUL5
BARX2
JRKL
ZNF259
MTMR2
USP2
HTR3B
ZW10
MMP20
UBE4A
MED17
EI24
FEZ1
CEP57
ARHGAP32
C2CD2L
RBM7
MPZL2
YAP1
HYOU1
ATP5L
GPR83
SRSF8
ADAMTS8
TREH
CEP164
IGSF9B
ENDOD1
EXPH5
PHLDB1
SIK2
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
CADM1
PANX1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
ACAD8
B3GAT1
DCPS
C11orf54
ZBTB44
THYN1
DDX25
NTM
CDON
SIDT2
TRAPPC4
CWC15
SPA17
FXYD6
CNTN5
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
ANKRD49
TTC12
C11orf57
ELMOD1
FOXRED1
KDM4D
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
IFT46
C11orf75
PRDM10
DSCAML1
GRAMD1B
KIAA1377
ARHGAP20
USP28
CARD18
AASDHPPT
PKNOX2
TP53AIP1
MMP27
ABCG4
ROBO3
C11orf1
TAF1D
RNF26
FAM118B
DYNC2H1
NLRX1
C11orf61
CCDC82
ALG9
CLMP
PDZD3
C11orf63
CCDC15
PDGFD
TMPRSS5
PUS3
MFRP
JAM3
BCO2
TMEM133
TMPRSS13
DCUN1D5
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
C11orf70
DIXDC1
KIAA1731
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
VPS26B
GLB1L3
TIRAP
CARD16
C1QTNF5
TMEM123
PANX3
APOA5
SLC36A4
FAT3
TMEM45B
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
FAM76B
SESN3
PIWIL4
ARHGAP42
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
AMOTL1
CCDC67
PATE1
C11orf65
ADAMTS15
MPZL3
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
HEPACAM
OAF
ANGPTL5
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
HEPHL1
C11orf34
VSTM5
FOLR4
KDM4DL
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
DDI1
BLID
CARD17
LINC00167
SCARNA9
HEPN1
LOC643037
LOC643733
LOC643923
CLDN25
LOC649133
RPL23AP64
SNORA8
SNORA1
SNORA18
SNORA40
SNORA25
SNORA32
SNORD5
SNORD6
LOC100128239
LOC100132078
PATE3
LOC100288077
LOC100288346
MIR1304
BACE1-AS
MIR4301
MIR3167
MIR1260B
LOC100499227
MIR3920
MIR3656
CASP12
LOC100507392
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4697
MIR4493
MIR4491
MIR4492
MIR4693
LOC100652768

Genes in Wide Peak

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

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

Genes
COL6A2
FTCD
C21orf56

Genes in Wide Peak

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

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

Genes
FOXK2
WDR45L

Genes in Wide Peak

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

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

Genes
DUX4
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
hsa-mir-1979
AGA
SLC25A4
CASP3
CLCN3
CPE
CTSO
DCTD
ETFDH
F11
ACSL1
FAT1
FRG1
GK3P
GLRB
GPM6A
GRIA2
GUCY1B3
HMGB2
HPGD
HSP90AA4P
ING2
IRF2
KLKB1
MTNR1A
NEK1
NPY1R
NPY5R
PPID
MSMO1
TDO2
TLL1
TLR3
VEGFC
GLRA3
SORBS2
SAP30
HAND2
RAPGEF2
MFAP3L
ADAM29
ANXA10
KLHL2
SCRG1
PALLD
ANP32C
FAM149A
FBXO8
DUX2
PDLIM3
SPOCK3
AADAT
FAM198B
ACCN5
GALNT7
CLDN22
C4orf27
MARCH1
NEIL3
TMEM144
C4orf43
UFSP2
DDX60
CDKN2AIP
ODZ3
LRP2BP
PDGFC
FSTL5
STOX2
KIAA1430
FNIP2
SH3RF1
RXFP1
SPCS3
TRAPPC11
MLF1IP
NBLA00301
WWC2
CEP44
SNX25
TKTL2
CBR4
MGC45800
DDX60L
NAF1
WDR17
ZFP42
SPATA4
ENPP6
ASB5
C4orf38
C4orf39
C4orf45
TRIM60
C4orf46
TMEM192
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC285501
LOC339975
TRIML1
LOC340017
ANKRD37
LOC389247
TRIM61
HELT
LOC401164
FAM92A3
HSP90AA6P
C4orf47
DUX4L4
GALNTL6
FRG2
SLED1
FLJ38576
DUX4L6
DUX4L5
DUX4L3
MIR578
LINC00290
LOC728175
DUX4L2
LOC731424
CLDN24
LOC100288255
MIR1305
MIR4276
MIR3945
MIR3688-1
LOC100505989
LOC100506013
LOC100506085
LOC100506122
LOC100506229
MIR3688-2

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
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
ACTA1
ACTN2
PARP1
ADSS
AGT
ARF1
ATF3
AVPR1B
C4BPA
C4BPB
CAPN2
CD34
CENPF
CHML
LYST
CHRM3
CR1
CR1L
CR2
CTSE
CD55
EIF2D
EPHX1
EPRS
ESRRG
GALNT2
GNG4
GUK1
H3F3A
HLX
HNRNPU
HSD11B1
IL10
IRF6
ITPKB
KCNH1
KCNK1
KCNK2
LAMB3
LBR
LGALS8
MARK1
CD46
MTR
NEK2
NID1
NVL
CDK18
PFKFB2
PIGR
PLXNA2
PPP2R5A
PROX1
PSEN2
PTPN14
RAB4A
RBBP5
RGS7
RYR2
SRP9
AURKAPS1
TARBP1
CNTN2
TBCE
TGFB2
LEFTY2
TLR5
GPR137B
TP53BP2
TRAF5
TSNAX
USH2A
WNT9A
ZNF124
SLC30A1
HIST3H3
GNPAT
DYRK3
CDC42BPA
DEGS1
KMO
RAB7L1
TAF1A
EXO1
FAIM3
MAPKAPK2
GGPS1
IKBKE
TMEM63A
TOMM20
URB2
CEP170
TMCC2
LPGAT1
AKT3
BPNT1
ZNF238
LEFTY1
SPHAR
CAPN9
SDCCAG8
IL24
DUSP10
COG2
RBM34
NFASC
FBXO28
SRGAP2
ABCB10
OPN3
DSTYK
RAB3GAP2
TRIM58
INTS7
AHCTF1
NSL1
OR1C1
OR2M4
OR2L2
OR2L1P
OR2T1
RPS6KC1
RNU5F-1
DIEXF
TAF5L
DISC2
DISC1
FLVCR1
CNIH4
PYCR2
NENF
IL19
G0S2
IL20
RRP15
PPPDE1
SCCPDH
TRIM17
KCTD3
DTL
ARID4B
EGLN1
KIAA1383
MARC2
SUSD4
KIF26B
GPATCH2
HEATR1
KLHDC8A
TMEM206
YOD1
BATF3
SLC30A10
ZNF692
IARS2
HHAT
ENAH
NUP133
RCOR3
SERTAD4
ERO1LB
FMN2
SMYD2
ADCK3
ZNF695
GJC2
CAMK1G
SIPA1L2
ZP4
RHOU
TFB2M
GREM2
NUCKS1
ACBD3
SMYD3
MARC1
ARV1
AIDA
JMJD4
C1orf116
C1orf35
TTC13
PGBD5
C1orf115
HHIPL2
VASH2
ZNF669
ZNF672
PCNXL2
WDR26
TRAF3IP3
SH3BP5L
OR2G3
OR2G2
OR2C3
TRIM11
NUAK2
RASSF5
MIXL1
C1orf124
FCAMR
OBSCN
NTPCR
EFCAB2
KIAA1804
LINC00467
ZNF496
C1orf198
DISP1
WNT3A
ANGEL2
HIST3H2A
LEMD1
ZNF670
NLRP3
SLC26A9
FAM36A
SNAP47
C1orf96
LYPLAL1
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
DNAH14
OR2B11
WDR64
C1orf131
SPATA17
EDARADD
MRPL55
HIST3H2BB
TATDN3
C1orf74
BROX
SLC35F3
LOC148696
B3GALNT2
MFSD4
PM20D1
C1orf150
LOC148824
CNIH3
LOC149134
EXOC8
RNF187
C1orf227
FAM71A
C1orf55
CNST
C1orf65
PLD5
C1orf100
IBA57
SLC41A1
OR2T6
LOC255654
SYT14
C1orf101
PGBD2
OR2L13
OR14A16
LOC284576
LOC284578
LOC284581
HNRNPU-AS1
LIN9
VN1R5
ZNF678
PRSS38
LOC339529
LOC339535
RD3
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
IRF2BP2
MIA3
C1orf95
FAM89A
TMEM81
CAPN8
C1orf31
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
C1orf140
FAM177B
ZNF847P
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MIR194-1
MIR205
MIR215
MIR29B2
MIR29C
C1orf186
TRIM67
MAP1LC3C
H3F3AP4
OR2W5
OR13G1
MIR135B
DUSP5P
C1orf133
MIR205HG
FLVCR1-AS1
LOC643723
SNRPD2P2
RPS7P5
LOC646627
SNORA14B
SNORA36B
SNORA16B
LOC728463
FAM72A
LOC731275
LOC100130093
LOC100130331
LOC100287814
LGALS8-AS1
MIR1182
MIR1537
MIR664
LINC00184
TSNAX-DISC1
MIR320B2
MIR3123
MIR3124
MIR4260
MIR3122
MIR3620
MIR3916
PROX1-AS1
LOC100506795
LOC100506810
ZNF670-ZNF695
MIR4753
MIR4666A
MIR4677
MIR4671
MIR4427
MIR4742
LINC00538

Genes in Wide Peak

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

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

Genes
ABL1
NOTCH1
RALGDS
TSC1
BRD3
NUP214
FNBP1
hsa-mir-602
hsa-mir-4292
hsa-mir-126
ABCA2
ABO
ASS1
C8G
CACNA1B
ENTPD2
CEL
CELP
COL5A1
DBH
SARDH
TOR1A
FCN1
FCN2
FUT7
RAPGEF1
GRIN1
LCN1
PAEP
PTGDS
RPL7A
RXRA
SNAPC4
SURF1
SURF2
SURF4
MED22
SURF6
TRAF2
TTF1
VAV2
LHX3
GFI1B
SSNA1
EDF1
FUBP3
CLIC3
GTF3C5
GTF3C4
MED27
PTGES
ADAMTSL2
PPP1R26
SEC16A
LAMC3
TUBB4B
UBAC1
OLFM1
AGPAT2
POMT1
SDCCAG3
NOXA1
USP20
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
MAN1B1
SETX
PMPCA
EXOSC2
NCS1
COBRA1
NELF
GPSM1
DKFZP434A062
GBGT1
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
NDOR1
TOR1B
METTL11A
PHPT1
ANAPC2
DPP7
OBP2B
OBP2A
MRPS2
EGFL7
PRRX2
C9orf78
FBXW5
C9orf167
EXD3
C9orf86
INPP5E
NPDC1
BARHL1
REXO4
KCNT1
GPR107
PRDM12
CARD9
DDX31
MRPL41
EHMT1
AIF1L
UCK1
NTNG2
PRRC2B
PPAPDC3
FIBCD1
KIAA1984
SNHG7
TMEM141
C9orf37
SAPCD2
C9orf69
UAP1L1
ARRDC1
WDR85
TMEM203
ZMYND19
NACC2
C9orf116
LCN8
FAM69B
ASB6
SLC34A3
CAMSAP1
C9orf163
MAMDC4
LCN6
AK8
C9orf96
QSOX2
LINC00094
LCN12
C9orf142
TPRN
FAM78A
QRFP
GLT6D1
C9orf50
PNPLA7
C9orf169
ENTPD8
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
LCN9
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
MIR126
C9orf106
LCN10
C9orf173
NRARP
FAM163B
FLJ40292
TUBBP5
RNF224
SNORA17
SNORA43
SNORD62B
MIR602
RNF208
DNLZ
LOC100128593
LOC100129722
LOC100130954
LOC100131193
FAM157B
RNU6ATAC
LOC100272217
LOC100289341
MIR4292
MIR3621
MIR3689A
MIR3689B
LOC100506190
LOC100506599
MIR3689D1
MIR3689F
MIR4669
MIR4673
MIR4674
MIR3689C
MIR3689D2
MIR3689E
MIR4479

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.33.

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

Genes
BCL3
ERCC2
CBLC
hsa-mir-150
hsa-mir-4324
hsa-mir-220c
hsa-mir-3191
hsa-mir-320e
hsa-mir-769
hsa-mir-642
AP2A1
APOC1
APOC1P1
APOC2
APOC4
APOE
BAX
BCAT2
C5AR1
CA11
CALM3
CD37
CGB
CKM
AP2S1
CLPTM1
CRX
DBP
DMPK
DMWD
EMP3
ERCC1
FCGRT
FLT3LG
FOSB
FTL
FUT1
FUT2
GIPR
GPR4
GRIN2D
ARHGAP35
GYS1
FOXA3
HRC
PRMT1
IRF3
KCNA7
KCNC3
KCNJ14
LHB
LIG1
BCAM
NOVA2
NPAS1
NTF4
NUCB1
PPP5C
PRRG2
PTGIR
PVR
PVRL2
RELB
RPL18
RPS11
RRAS
RTN2
SEPW1
SLC1A5
SLC8A2
SNRNP70
SNRPD2
SULT2B1
SULT2A1
TULP2
VASP
ZNF45
ZNF221
ZNF222
ZNF155
ZNF180
ZNF223
ZNF224
ZNF225
ZNF226
ZNF227
ZFP112
ZNF229
ZNF230
SYMPK
TEAD2
PPFIA3
PLA2G4C
NAPA
PGLYRP1
CYTH2
ZNF235
DHX34
SAE1
TOMM40
ZNF234
PPP1R13L
CD3EAP
RUVBL2
KDELR1
CLASRP
KPTN
PNKP
ATF5
CARD8
ZC3H4
FBXO46
RPL13A
SYNGR4
NUP62
PPP1R15A
EML2
PRKD2
ZNF473
CCDC9
IRF2BP1
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
ZNF285
BBC3
DKKL1
GPR77
DHDH
SLC6A16
STRN4
GLTSCR2
GLTSCR1
EHD2
NOSIP
HSD17B14
VRK3
PTOV1
TRPM4
QPCTL
FAM83E
RASIP1
TMEM160
PIH1D1
C19orf73
PNMAL1
TMEM143
CABP5
SPHK2
MEIS3
CEACAM19
SLC17A7
RCN3
PNMAL2
PRR12
PLEKHA4
MARK4
SCAF1
TSKS
ELSPBP1
LIN7B
HIF3A
TRAPPC6A
FKRP
TBC1D17
GEMIN7
MYH14
FUZ
OPA3
RSPH6A
MED25
BCL2L12
GRWD1
CCDC8
ZNF541
AKT1S1
SNORD35B
EXOC3L2
CCDC114
DKFZp434J0226
CGB5
CGB7
CGB8
GNG8
PTH2
SIGLEC11
CGB1
CGB2
LMTK3
CEACAM20
IZUMO2
CPT1C
ALDH16A1
NTN5
PPM1N
KLC3
IGSF23
CCDC155
DACT3
SIX5
IGFL2
ZNF296
ZNF114
SPACA4
C19orf76
PRR24
IL4I1
PPP1R37
NKPD1
TPRX1
MAMSTR
IZUMO1
MYPOP
NANOS2
ZNF284
ZNF233
IGFL1
CEACAM22P
CEACAM16
BLOC1S3
LOC388553
IGFL3
SIGLEC16
FLJ26850
MIR150
MIR330
IGFL4
SEC1
SNORD23
MIR642A
RPL13AP5
CCDC61
MIR769
SNAR-G1
SNAR-A1
SNAR-A2
SNAR-A12
BSPH1
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-B2
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-B1
SNAR-C1
SNAR-C3
SNAR-D
SNAR-G2
SNAR-A14
LOC100287177
LOC100379224
MIR3191
MIR3190
MIR320E
MIR4324
MIR642B
LOC100505681
LOC100505715
LOC100505812
LOC100506012
LOC100506033
LOC100506068
LOC100507003
APOC4-APOC2
MIR4749
MIR4750
MIR4531
MIR4751

Genes in Wide Peak

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

Table S27. 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
KIF21A
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 3q25.1.

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

Genes
FOXL2
MLF1
GMPS
hsa-mir-1263
hsa-mir-16-2
AADAC
AGTR1
ATP1B3
ATR
CP
CPA3
CPB1
GYG1
IL12A
KPNA4
TM4SF1
MBNL1
MME
NCK1
P2RY1
PCCB
PFN2
PIK3CB
PLOD2
PLS1
PLSCR1
PPP2R3A
PTX3
RAP2B
RARRES1
RASA2
RBP1
RBP2
SHOX2
SIAH2
HLTF
SSR3
TFDP2
TM4SF4
TRPC1
CLRN1
ZIC1
KCNAB1
SOX14
B3GALNT1
SLC33A1
COPB2
CHST2
RNF7
TSC22D2
P2RY14
SMC4
STAG1
RNF13
MRAS
PLCH1
U2SURP
ARMC8
WWTR1
TIPARP
ARHGEF26
PCOLCE2
SERP1
GPR171
SCHIP1
NMD3
COMMD2
A4GNT
DBR1
CLDN18
RSRC1
SELT
P2RY13
IL20RB
GPR87
XRN1
MSL2
FAIM
SLC25A36
SUCNR1
LXN
MRPS22
CCNL1
PLSCR2
PLSCR4
IFT80
BPESC1
CLSTN2
MFSD1
P2RY12
VEPH1
ARL14
CEP70
TMEM22
ESYT3
EIF2A
ZIC4
HPS3
GFM1
SPSB4
ACPL2
TM4SF18
MED12L
CLRN1-AS1
OTOL1
FAM194A
GRK7
PISRT1
PPM1L
C3orf55
C3orf79
SPTSSB
DHX36
DZIP1L
LOC201651
C3orf58
ZBTB38
GK5
SLC9A9
IGSF10
C3orf33
TRIM59
TRIM42
LOC339894
AADACL2
GPR149
PAQR9
NME9
NMNAT3
PRR23B
PRR23C
PLSCR5
ANKUB1
LEKR1
C3orf72
LOC401093
C3orf80
MIR15B
MIR16-2
TMEM14E
LOC646903
PA2G4P4
LOC647107
IQCJ
SCARNA7
PRR23A
LOC730091
WWTR1-AS1
TIPARP-AS1
LOC100289361
MIR548H2
LOC100498859
MIR3919
IQCJ-SCHIP1
LOC100507389
ARHGEF26-AS1
LOC100507537

Genes in Wide Peak

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

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

Genes
ZMYND11
DIP2C
TUBB8
C10orf108

Genes in Wide Peak

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

Table S30. 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 8p23.2.

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

Genes
hsa-mir-548i-3
hsa-mir-596
ANGPT2
DEFA1
DEFA3
DEFA4
DEFA5
DEFA6
DEFB1
DEFB4A
CLN8
MYOM2
DLGAP2
MFHAS1
ARHGEF10
KBTBD11
SPAG11B
FBXO25
AGPAT5
DEFB103B
CSMD1
MCPH1
PPP1R3B
ERI1
CLDN23
DEFB104A
LOC157273
SGK223
C8orf42
ERICH1
ZNF596
DEFT1P
DEFB105A
DEFB106A
DEFB107A
FLJ10661
LOC286083
LOC349196
XKR5
DEFB103A
OR4F21
FAM90A13
FAM90A5
FAM90A7
FAM90A8
FAM90A18
FAM90A9
FAM90A10
DEFA10P
DEFB107B
DEFB104B
DEFB106B
DEFB105B
DEFB109P1B
RPL23AP53
FAM90A14
SPAG11A
MIR596
DEFA1B
FAM90A20
FAM90A19
FAM66B
ZNF705G
FAM66E
LOC100132396
LOC100287015
DEFT1P2
DEFB4B
MIR548I3
MIR4659A
MIR4660
MIR4659B
LOC100652791

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p32.3.

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

Genes
CDKN2C
FAF1
DMRTA2

Genes in Wide Peak

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

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

Genes
GNA11
STK11
TCF3
FSTL3
hsa-mir-4321
hsa-mir-1909
hsa-mir-3187
hsa-mir-1302-11
AES
AMH
ATP5D
AZU1
HCN2
BSG
CDC34
CIRBP
CNN2
CSNK1G2
CFD
ARID3A
EFNA2
ELANE
GAMT
GNA15
GNG7
MKNK2
GPX4
GZMM
GADD45B
OAZ1
PALM
POLR2E
POLRMT
PRTN3
PTBP1
RPS15
SGTA
THOP1
TLE2
MADCAM1
SF3A2
PPAP2C
S1PR4
AP3D1
MED16
APC2
ABCA7
UQCR11
SBNO2
HMHA1
SHC2
TIMM13
DAZAP1
FGF22
SLC39A3
THEG
LSM7
MBD3
MIER2
PCSK4
C19orf24
PLEKHJ1
BTBD2
RNF126
SPPL2B
WDR18
REXO1
ZNF77
TLE6
LPPR3
ZNF556
OR4F17
FAM108A1
KLF16
DOT1L
KISS1R
LMNB2
MUM1
MIDN
R3HDM4
C19orf6
TPGS1
REEP6
IZUMO4
SCAMP4
ADAT3
ZNF554
GRIN3B
ZNF57
JSRP1
MOB3A
C19orf21
PLK5
C2CD4C
CIRBP-AS1
C19orf25
ATP8B3
DIRAS1
ZNF555
C19orf26
CSNK1G2-AS1
ODF3L2
ADAMTSL5
TMPRSS9
NDUFS7
C19orf35
WASH5P
ONECUT3
MEX3D
FLJ45445
PRSS57
FAM138F
LINGO3
FAM138A
LOC100288123
MIR1909
MIR1227
MIR3187
MIR4321
MIR4745

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 14q24.1.

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

Genes
KTN1
NKX2-1
TSHR
TCL1A
TRIP11
GOLGA5
GPHN
DICER1
TCL6
NIN
CCNB1IP1
BCL11B
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-345
hsa-mir-342
hsa-mir-3173
hsa-mir-1260
hsa-mir-625
hsa-mir-548h-1
hsa-mir-4308
hsa-mir-3172
hsa-mir-624
hsa-mir-3171
hsa-mir-4307
hsa-mir-208b
hsa-mir-1201
SERPINA3
ACTN1
ACYP1
ANG
APEX1
ARF6
ARG2
ARHGAP5
BCL2L2
BDKRB1
BDKRB2
BMP4
ZFP36L1
CALM1
SERPINA6
ENTPD5
CDKN3
CEBPE
CFL2
FOXN3
CHGA
CMA1
LTB4R
CTSG
DAD1
COCH
DIO2
DIO3
DLST
DYNC1H1
EIF2S1
EML1
ERH
ESR2
ESRRB
FKBP3
FOXG1
FNTB
FOS
FUT8
GALC
GCH1
GMFB
GPR33
GPX2
GSTZ1
GTF2A1
GZMH
GZMB
HIF1A
FOXA1
HNRNPC
HSPA2
IFI27
ITPK1
LGALS3
LTBP2
MAX
MGAT2
CTAGE5
ATXN3
MAP3K9
MMP14
ALDH6A1
MNAT1
MTHFD1
MYH6
MYH7
NDUFB1
NEDD8
NFATC4
NFKBIA
NOVA1
PNP
NRL
SIX6
OTX2
OXA1L
PAX9
SERPINA5
PCK2
PGF
SERPINA1
SERPINA4
PIGH
PNN
POLE2
PPM1A
PPP2R5C
PPP2R5E
PRKCH
PRKD1
LGMN
PSEN1
PSMA3
PSMA6
PSMB5
PSMC1
PSMC6
PSME1
PSME2
PTGDR
PTGER2
ABCD4
PYGL
RABGGTA
RAD51B
ARID4A
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
RPL36AL
RPS29
RTN1
SALL2
SEL1L
SRSF5
SIX1
SLC8A3
SLC10A1
SNAPC1
SOS2
SPTB
SRP54
SSTR1
STYX
TEP1
TGFB3
TGM1
VRK1
WARS
YY1
ZBTB25
PABPN1
DPF3
GPR68
GPR65
GEMIN2
NUMB
ADAM21
ADAM20
DLK1
CCNK
CDKL1
DCAF5
ALKBH1
EIF2B2
AP1G2
SLC7A7
NEMF
PNMA1
RPS6KA5
CPNE6
NRXN3
AKAP6
AKAP5
SPTLC2
TCL1B
RGS6
KIAA0391
KIAA0247
KIAA0586
DLGAP5
KIAA0317
TOX4
REC8
MED6
PARP2
CNIH
DHRS2
EFS
IRF9
PRMT5
SEC23A
VTI1B
FBLN5
BATF
TM9SF1
NPC2
AHSA1
EXOC5
CGRRF1
CYP46A1
EDDM3A
DHRS4
PAPOLA
ACOT2
TMED10
FERMT2
RIPK3
PTPN21
AP4S1
C14orf1
WDHD1
BAZ1A
MAP4K5
SUPT16H
NID2
VASH1
ATG14
ZBTB1
SNW1
ACIN1
PCNX
DAAM1
SAMD4A
TTLL5
FAM179B
SYNE2
SCFD1
KHNYN
ANGEL1
SLC7A8
ZFYVE26
TTC9
KLHDC2
FLRT2
HECTD1
HEATR5A
NGDN
LRP10
PLEKHG3
SIPA1L1
DCAF4
C14orf109
NKX2-8
TINF2
PLEK2
TIMM9
OR10G3
OR10G2
OR4E2
MLH3
ATP5S
KCNH5
CIDEB
PRO1768
CHMP4A
STXBP6
POMT2
STRN3
SLC39A2
ERO1L
COQ6
FAM158A
ATL1
FCF1
RDH11
SERPINA10
GLRX5
ZNF219
COX16
GMPR2
SLC22A17
DACT1
ATP6V1D
EVL
C14orf129
JKAMP
MBIP
DHRS7
C14orf166
ASB2
SIX4
ZFYVE1
CPSF2
KCNK10
GNG2
KLHL28
C14orf101
HAUS4
PPP2R3C
PRPF39
C14orf119
FBXO34
C14orf102
RNF31
ATG2B
RBM23
UBR7
DNAAF2
C14orf105
EXD2
VRTN
MIS18BP1
SYNJ2BP
SLC39A9
MEG3
C14orf167
G2E3
FLVCR2
OSGEP
C14orf118
SMEK1
ARHGEF40
BTBD7
MUDENG
TDP1
SPATA7
EAPP
ACTR10
YLPM1
METTL3
LTB4R2
KCNK13
C14orf162
SDR39U1
C14orf132
DDX24
RPGRIP1
ADCK1
TMEM63C
PELI2
RHOJ
NDRG2
GALNTL1
PLEKHH1
NYNRIN
TXNDC16
TRMT5
UNC79
HOMEZ
BEGAIN
CHD8
FANCM
PPP4R4
ZNF410
NGB
RBM25
SNX6
SAV1
C14orf93
ABHD4
C14orf133
NPAS3
SMOC1
MOAP1
DIO3OS
EDDM3B
IRF2BPL
MPP5
CDH24
C14orf135
GPR135
METTL17
IL25
GNPNAT1
OTUB2
MEG8
THTPA
OR4K5
OR11H2
WDR25
OR4K1
METTL21D
LINC00341
ZC2HC1C
C14orf169
IPO4
CLMN
CATSPERB
ZC3H14
RIN3
L2HGDH
C14orf159
C14orf45
NUBPL
DCAF11
DDHD1
OR4K15
SGPP1
TMX1
SLIRP
DNAL1
RPS6KL1
SYT16
IFI27L2
FSCB
SETD3
BRMS1L
HHIPL1
JPH4
C14orf142
RNASE7
INSM2
ARHGAP5-AS1
RAB2B
AJUBA
STON2
ZFHX2
KIAA1737
RPPH1
SLC25A21
PAPLN
FAM181A
EFCAB11
LRRC16B
PPP1R3E
TMEM55B
CHURC1
C14orf43
LIN52
NEK9
TTC5
MAPK1IP1L
EGLN3
C14orf126
IFT43
WDR89
C14orf149
TRIM9
DHRS1
CMTM5
MIA2
AK7
IFI27L1
C14orf28
TRAPPC6B
RNASE11
TPPP2
RNASE8
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
LRR1
KLHDC1
FRMD6
SOCS4
NAA30
GPHB5
NOXRED1
JDP2
ISCA2
ACOT4
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
KLHL33
RPL10L
LINC00239
RDH12
ADAM21P1
GSC
SERPINA12
PRIMA1
MIPOL1
PPP1R36
SLC38A6
C14orf37
FRMD6-AS1
ABHD12B
LOC145474
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
MDP1
TTC7B
LRFN5
FAM71D
TMEM229B
C14orf49
CLEC14A
FITM1
REM2
TMEM30B
MDGA2
SAMD15
C14orf21
EML5
SPTSSA
ADCY4
C14orf183
RALGAPA1
SFTA3
FBXO33
LINC00521
SERPINA11
IGBP1P1
LOC283547
C14orf182
LOC283553
GPR137C
PROX2
ZDHHC22
TMED8
C14orf178
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
LOC283624
TSSK4
FAM177A1
DHRS4L2
C14orf55
C14orf39
CCDC85C
ITPK1-AS1
SNORD8
SNORD56B
SERPINA9
RNASE10
VSX2
OR6S1
SLC35F4
COX8C
RAB15
FLJ31306
TBPL2
C14orf23
TOMM20L
SERPINA13
C14orf64
RTL1
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
HEATR4
FLJ22447
PLEKHD1
LOC400236
LOC400238
DICER1-AS1
POTEG
MIR127
MIR134
MIR136
MIR154
MIR208A
MIR299
C14orf165
OR11H12
RNASE13
LINC00238
CCDC88C
OR4Q3
OR4M1
TEX21P
MIR323A
MIR337
MIR345
MIR376C
MIR369
RNASE12
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR323B
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
ACOT1
ACOT6
POTEM
LOC642426
ECRP
C14orf176
CBLN3
LOC645431
RPL13AP3
LINC00520
FLJ43390
SYNDIG1L
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA79
SNORD9
MIR411
MIR624
MIR654
MIR655
MIR656
DHRS4L1
C14orf38
LOC731223
SNORD113-1
SNORD113-2
SNORD113-4
SNORD113-5
SNORD113-6
SNORD113-7
SNORD113-9
SNORD114-1
SNORD114-2
SNORD114-3
SNORD114-4
SNORD114-5
SNORD114-6
SNORD114-7
SNORD114-8
SNORD114-9
SNORD114-10
SNORD114-11
SNORD114-12
SNORD114-13
SNORD114-14
SNORD114-15
SNORD114-16
SNORD114-17
SNORD114-18
SNORD114-19
SNORD114-20
SNORD114-21
SNORD114-22
SNORD114-23
SNORD114-24
SNORD114-25
SNORD114-26
SNORD114-27
SNORD114-28
SNORD114-29
SNORD114-30
SNORD114-31
MIR758
MIR668
MIR770
SNORD127
SNORD126
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR208B
MIR889
KTN1-AS1
LOC100129345
LOC100129794
LOC100288846
LOC100289511
MIR1247
MIR1185-1
MIR1185-2
MIR1260A
MIR1197
OTX2OS1
MIR1193
MIR3173
MIR4308
MIR4307
MIR548Y
LOC100505967
LOC100506071
LOC100506321
LOC100506433
LOC100507043
NEDD8-MDP1
BCL2L2-PABPN1
SYNJ2BP-COX16
CHURC1-FNTB
MIR4505
MIR4708
MIR4709
MIR4503
MIR548AI
MIR4707
MIR4706
MIR2392
LOC100628307
HIF1A-AS2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.32.

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p21.31.

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

Genes
CTNNB1
FHIT
MITF
MLH1
MYD88
BAP1
FOXP1
SETD2
PBRM1
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
ACAA1
ACVR2B
ACY1
ALAS1
AMT
APEH
ARF4
RHOA
C3orf51
CACNA1D
SLC25A20
CAMP
CCK
ENTPD3
CDC25A
CISH
CCR1
CCR3
CCR4
CCR5
CCR8
CCBP2
COL7A1
CX3CR1
CYP8B1
DAG1
DNASE1L3
DOCK3
DUSP7
CELSR3
FLNB
GBE1
GLB1
GNAI2
GNAT1
GOLGA4
XCR1
GPR27
GPX1
GRM2
HYAL1
IMPDH2
ITGA9
ITIH1
ITIH3
ITIH4
LAMB2
RPSA
LTF
MAP4
MOBP
MST1
MST1R
MYL3
NKTR
CNTN3
PDHB
PFKFB4
PLCD1
PLXNB1
POU1F1
PRKAR2A
PRKCD
PTH1R
PTPRG
QARS
RARB
SNORA62
ROBO1
ROBO2
RPL29
ATXN7
SCN5A
SCN10A
SEMA3F
SMARCC1
STAC
NEK4
TCTA
TDGF1
TGM4
TGFBR2
THRB
TKT
TMF1
CLEC3B
TNNC1
TOP2B
UBA7
UBP1
USP4
UQCRC1
VIPR1
WNT5A
ZNF35
IFRD2
MAPKAPK3
SEMA3B
SLMAP
MANF
ACOX2
EOMES
HYAL3
CADPS
HYAL2
SUCLG2
HESX1
BSN
LIMD1
CCRL2
UBA3
RPL14
SEC22C
RRP9
LRRFIP2
MAGI1
CACNA2D2
SLC22A14
SLC22A13
SLC4A7
VPRBP
IP6K1
EPM2AIP1
PSMD6
TRANK1
DLEC1
EXOG
XYLB
OXSR1
NR1D2
PDCD6IP
PARP3
ZNF197
RBM6
RBM5
NME6
CTDSPL
EIF1B
TRAIP
ARIH2
CRTAP
ARL6IP5
NPRL2
CXCR6
CSPG5
ARPP21
CCR9
USP19
SLC38A3
CYB561D2
TMEM115
RPP14
FAM107A
WDR6
RASSF1
NISCH
TREX1
SCN11A
TUSC2
TWF2
TRAK1
DHX30
SACM1L
SCAP
LAMB2P1
EXOSC7
PDZRN3
CLASP2
RAD54L2
FRMD4B
STAB1
GPD1L
NBEAL2
FAM208A
KLHL18
LARS2
RYBP
NAT6
FBXL2
ABHD14A
POC1A
CNOT10
TMEM158
NDUFAF3
MYRIP
PTPN23
CHMP2B
DNAH1
HIGD1A
LRIG1
SUSD5
ERC2
APPL1
GNL3
RBMS3
SPCS1
PRSS50
RBM15B
GMPPB
ARHGEF3
VILL
ABHD5
DYNC1LI1
C3orf18
SS18L2
SHISA5
ZDHHC3
ZMYND10
TEX264
CCDC72
ZNF589
HEMK1
IP6K2
SFMBT1
NCKIPSD
PHF7
TLR9
LZTFL1
P4HTM
SLC6A20
IL17RD
C3orf75
SNRK
QRICH1
PXK
CMTM6
SLC25A38
ULK4
OXSM
FEZF2
EBLN2
ANO10
DALRD3
SHQ1
CHDH
IL17RB
NGLY1
CACNA2D3
DCP1A
GLT8D1
ZNF167
LMOD3
SEMA3G
KIF15
ADAMTS9
PCBP4
ABHD6
LRTM1
C3orf14
KIAA1143
HHATL
WDR48
SELK
PROK2
RNF123
KIF9
AZI2
CSRNP1
GORASP1
CDCP1
CCDC71
NT5DC2
SLC26A6
CAMKV
LRRC2
FYCO1
CCDC51
THOC7
WDR82
RTP3
ID2B
ATRIP
NICN1
MON1A
KBTBD8
ABHD14B
C3orf39
DCLK3
UCN2
ZNF502
RFT1
ZBTB47
ACTR8
CMTM7
OSBPL10
SLC25A26
ZNF501
LRRC3B
GPR62
FAM3D
LYZL4
KBTBD5
TRIM71
TMEM42
IQCF1
GLYCTK
PPM1M
C3orf49
SNTN
SYNPR
C3orf45
ASB14
FAM19A4
CCDC12
PPP4R2
LOC152024
ZCWPW2
CMC1
NEK10
CMTM8
CCDC13
XIRP1
PRICKLE2
TTC21A
C3orf67
KCTD6
KLHDC8B
STT3B
LOC201617
DNAH12
PDE12
FAM116A
CADM2
ZNF620
ALS2CL
TMIE
C3orf64
FBXW12
ENTPD3-AS1
ZNF619
ZNF621
LOC285326
CCDC66
C3orf23
ZNF660
FLJ39534
LOC285401
EIF4E3
CCDC36
C3orf35
GADL1
PRSS42
ZNF860
ZNF445
SPATA12
C3orf77
C3orf62
TMEM110
PRSS45
AMIGO3
ZNF662
CDHR4
FAM212A
IQCF2
IQCF5
MUSTN1
VGLL3
IQCF3
LOC401074
MIRLET7G
MIR128-2
MIR135A1
MIR138-1
MIR191
MIR26A1
FAM19A1
FLJ33065
TMEM89
IQCF6
C3orf78
LOC440970
MIR425
SNORA6
TMPPE
LOC644714
LOC644990
LOC645206
SPINK8
C3orf71
LOC646498
FLJ20518
SNORD19
FAM86DP
SNORD69
MIR548A2
MIR564
GXYLT2
FAM198A
CCR2
ESRG
SNORD19B
C3orf74
LOC100128640
NRADDP
ZNF717
LOC100132146
BSN-AS2
PRSS46
LOC100287879
FRG2C
MIR1284
MIR1324
MIR1226
MIR711
MIR3136
MIR4272
MIR4271
MIR4273
MIR3938
KRBOX1
IQCF4
LOC100506994
LOC100507062
ADAMTS9-AS2
ABHD14A-ACY1
TMEM110-MUSTN1
MIR4793
MIR4787
MIR4795
MIR4444-1
MIR4443
MIR4792
MIR4442
LOC100652759
LUST

Genes in Wide Peak

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

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

Genes
PRDM1
MLLT4
MYB
ROS1
TNFAIP3
STL
FGFR1OP
GOPC
hsa-mir-1913
hsa-mir-1202
hsa-mir-1273c
hsa-mir-3145
hsa-mir-548a-2
hsa-mir-588
hsa-mir-3144
hsa-mir-548b
hsa-mir-587
hsa-mir-2113
hsa-mir-4282
hsa-mir-30a
hsa-mir-30c-2
hsa-mir-548u
hsa-mir-133b
ACAT2
CRISP1
AIM1
AMD1
ARG1
BAI3
BCKDHB
BMP5
DST
CCNC
CGA
CCR6
CNR1
COL9A1
COL10A1
COL12A1
COL19A1
COX7A2
CTGF
EEF1A1
EPB41L2
EPHA7
EYA4
ESR1
FABP7
FOXO3
FRK
FUCA2
FYN
GABRR1
GABRR2
GJA1
GCLC
GPR6
GPR31
GRIK2
GRM1
GSTA1
GSTA2
GSTA3
GSTA4
HCRTR2
HDAC2
HIVEP2
HSF2
HTR1B
HTR1E
IFNGR1
IGF2R
IL17A
IMPG1
KIF25
KPNA5
LAMA2
LAMA4
LPA
MARCKS
MAN1A1
MAS1
MCM3
ME1
MAP3K4
MAP3K5
MUT
MYO6
NMBR
NT5E
OPRM1
PARK2
PCMT1
PDCD2
ENPP1
ENPP3
PEX7
PGK2
PGM3
PKHD1
PLAGL1
PLG
PLN
POU3F2
PREP
PRIM2
PKIB
PSMB1
PTPRK
REV3L
RHAG
RNY4
RPS6KA2
RPS12
SGK1
SIM1
SLC22A1
SLC22A3
SLC22A2
SMPD2
SOD2
ELOVL4
T
MAP3K7
TBP
TCF21
TCP1
TCP10
TCTE3
DYNLT1
TFAP2B
THBS2
NR2E1
TPBG
TPD52L1
CRISP2
TSPYL1
TTK
UTRN
EZR
VIP
PTP4A1
EPM2A
STX7
PEX3
GCM1
DDO
RNASET2
STX11
SNX3
RNGTT
CD164
WISP3
SYNJ2
VNN2
VNN1
WASF1
TAAR5
MAP7
TBX18
LATS1
TAAR2
TAAR3
HMGN3
MED23
QKI
FHL5
AKAP7
ATG5
TBPL1
BAG2
WTAP
AKAP12
TRAM2
KIAA0408
PHACTR2
BCLAF1
ZBTB24
SNAP91
FIG4
CASP8AP2
UST
CRISP3
TRDN
CITED2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
HBS1L
PDE10A
SMPDL3A
PNRC1
ASCC3
RAB32
KATNA1
BVES
SEC63
SCAF8
KIAA1009
ICK
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
TAB2
MDN1
TSPYL4
SASH1
SYNE1
UFL1
PHF3
HEY2
HEBP2
ORC3
BRD7P3
MTO1
ASF1A
CCDC28A
MTHFD1L
PNISR
IBTK
MOXD1
IPCEF1
ZNF451
SENP6
TIAM2
FBXL4
C6orf123
FBXO9
FBXO5
SLC17A5
RGS17
SNORD50A
PDE7B
FILIP1
SESN1
TINAG
DLL1
OSTM1
TMEM14A
MRPL18
NDUFAF4
DSE
CLDN20
NOX3
HDDC2
TFB1M
CYB5R4
TUBE1
C6orf203
CDC40
RWDD1
AIG1
SNX9
UBE2J1
VTA1
LGSN
BRP44L
HECA
RAB23
COQ3
IL20RA
UNC93A
HMGCLL1
MTRF1L
AHI1
RMND1
PHIP
SOBP
AKIRIN2
CENPQ
LRRC1
PHF10
QRSL1
VNN3
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
C6orf70
LMBRD1
ECHDC1
KCNQ5
AGPAT4
TULP4
RARS2
HYMAI
PDSS2
C6orf162
GPR126
KIAA1244
NHSL1
LYRM2
SNX14
PLEKHG1
ARID1B
SERINC1
HACE1
FAM135A
TMEM181
ZBTB2
BEND3
KIAA1586
C6orf115
RRAGD
PRDM13
PBOV1
BACH2
ELOVL5
TRMT11
SMAP1
C6orf164
PERP
SMOC2
POPDC3
ALDH8A1
MICAL1
ULBP3
OR2A4
C6orf211
OGFRL1
FAM184A
ZDHHC14
MANEA
ADGB
LINC00472
FRMD1
AGPAT4-IT1
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
KHDC1
GPR63
COL21A1
PPP1R14C
SPACA1
RNF146
SF3B5
TAAR8
SH3BGRL2
TFAP2D
RSPH3
TTLL2
ARMC2
FBXO30
RPF2
L3MBTL3
FAM120B
MCHR2
FAXC
FNDC1
GJA10
RTN4IP1
RSPO3
LRP11
LTV1
SERAC1
USP45
REPS1
PPIL4
PAQR8
SLC22A16
C6orf7
UBE2CBP
MLIP
LINC00473
KIAA1919
ARHGAP18
SYTL3
GTF3C6
MRAP2
RWDD2A
IL17F
FAM54A
SFT2D1
EFHC1
KLHL32
TMEM200A
MB21D1
NUS1
C6orf72
IL22RA2
C6orf192
SLC16A10
TAGAP
ADAT2
RIPPLY2
IRAK1BP1
CLVS2
TAAR9
TAAR1
STXBP5
NCOA7
HINT3
PACRG
B3GAT2
C6orf57
CD109
RAET1E
PM20D2
SRSF12
C6orf141
LOC153910
ZC2HC1B
CNKSR3
RAET1L
SAMD3
MGC34034
SLC2A12
LOC154092
PNLDC1
RNF217
NKAIN2
C6orf221
C6orf165
BVES-AS1
LOC154449
PRSS35
LCA5
OLIG3
TXLNB
DACT2
C6orf118
OSTCP1
KHDRBS2
C6orf163
CCDC162P
AKD1
NT5DC1
FAM26D
ZUFSP
FAM162B
C6orf170
BEND6
GSTA5
HS3ST5
GPRC6A
RFX6
SLC35F1
FAM83B
VGLL2
DEFB110
DEFB112
DEFB113
DEFB114
LACE1
C6orf191
MMS22L
WDR27
FAM26E
MCM9
SCML4
SHPRH
LINC00326
LOC285740
CEP57L1
PPIL6
LOC285758
FLJ34503
DCBLD1
LOC285762
LOC285796
PRR18
TAAR6
SLC35D3
ZC3H12D
DPPA5
RSPH4A
ECT2L
EYS
NUP43
C6orf58
RAET1G
GUSBP4
GJB7
HMGA1P7
SNHG5
SUMO4
C6orf147
CENPW
C6orf174
LINC00222
CEP85L
C6orf120
THEMIS
GLYATL3
GFRAL
LIN28B
SAMD5
IYD
KLHL31
DKFZp451B082
TCP10L2
LINC00242
DEFB133
GTF2H5
MIR206
MIR30A
MIR30C2
OOEP
FAM26F
FLJ46906
LOC441177
PTCHD4
MCART3P
GSTM2P1
RFPL4B
MIR133B
SNORD101
SNORD100
SNORA33
C6orf225
TSG1
LOC643623
TRAF3IP2-AS1
CTAGE9
LOC645434
RAET1K
RPS16P5
MLLT4-AS1
SNORA20
SNORA29
SNORD50B
MIR548B
LOC728012
TPI1P3
C6orf186
LOC729176
LOC729178
TMEM242
LOC729603
LOC730101
GSTA7P
HGC6.3
LOC100128176
BET3L
KHDC1L
LOC100129518
LOC100130890
C6orf99
LINC00271
LOC100132735
LOC100287632
LOC100288198
LOC100289495
NHEG1
MIR1913
MIR2113
MIR548H3
LOC100422737
MIR3145
MIR4282
MIR3918
MIR3939
MIR3668
MIR3662
MIR3692
LOC100506804
LOC100507203
LOC100507254
LOC100507462
LOC100507489
LOC100507557
CAHM
MIR4464
MIR4466
MIR4643
MIR4465
MIR4644
LOC100652739

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7q36.3.

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

Genes
BRAF
EZH2
MET
SMO
KIAA1549
MLL3
CREB3L2
hsa-mir-595
hsa-mir-153-2
hsa-mir-671
hsa-mir-1975
hsa-mir-548f-4
hsa-mir-490
hsa-mir-29b-1
hsa-mir-335
hsa-mir-183
hsa-mir-129-1
hsa-mir-593
hsa-mir-592
ABP1
AKR1B1
ARF5
OPN1SW
BPGM
CALD1
CALU
CAPZA2
CASP2
CAV1
CAV2
CDK5
CFTR
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GPR37
GRM8
MNX1
HTR5A
IMPDH1
INSIG1
IRF5
KCND2
KCNH2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PPP1R3A
PRSS1
PRSS2
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SHH
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
WNT2
XRCC2
ZYX
ST7
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ACCN3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
AASS
FAM3C
FASTK
ABCB8
TFEC
PAXIP1
KLHDC10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
TSPAN12
CLEC5A
MKRN1
POT1
CNTNAP2
HYALP1
TES
GIMAP2
OR2F1
SLC13A4
COPG2
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
MDFIC
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
LUC7L2
MRPS33
NUB1
NAA38
TAS2R5
CHPF2
ING3
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
METTL2B
TRPV5
ANKRD7
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
FAM40B
ESYT2
ZNF398
EXOC4
GALNT11
LRRC4
LMBR1
LINC00244
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
C7orf58
TTC26
JHDM1D
TMUB1
CTTNBP2
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
LOC93432
ST7-AS1
ST7-AS2
ST7-OT3
CADPS2
CPA5
FOXP2
CEP41
C7orf29
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
PRSS58
ASZ1
RNF32
ASB15
TRY6
LOC154761
CLEC2L
C7orf55
LOC154822
LOC154860
IQUB
LOC154872
TMEM213
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
RBM33
MGC27345
GALNTL5
RNF133
GIMAP7
ZNF467
ZNF800
GIMAP1
LOC202781
C7orf33
FABP5P3
UBN2
TAS2R39
TAS2R40
TAS2R41
CNPY1
LOC285889
FLJ40852
LOC285965
FAM115C
ZNF775
LOC285972
ATG9B
TPI1P2
FLJ40288
MESTIT1
ST7-OT4
TAS2R60
CTAGE6P
TSPAN33
AGBL3
OR6V1
OR2A12
OR2A1
FAM71F2
STRA8
KLRG2
WDR86
LOC349160
GSTK1
KCP
FLJ43663
RNF148
FEZF1
FAM180A
OR2A25
OR2A5
PRRT4
RAB19
OR2A7
OR2A20P
LOC401431
OR2A42
FLJ45340
MIR129-1
MIR153-2
MIR182
MIR183
MIR29A
MIR29B1
MIR96
LOC407835
AKR1B15
CTAGE15P
OR2A9P
OR2A2
LMOD2
MIR335
ARHGEF35
GIMAP6
WEE2
MIR490
ZNF862
LOC645249
LOC646329
C7orf73
ACTR3C
MIR592
MIR593
MIR595
LOC728377
LOC728743
TMEM229A
LOC730441
LUZP6
MIR671
LOC100124692
LOC100128264
CTAGE4
LOC100128822
LOC100129148
LOC100130705
LOC100130880
LOC100131176
LOC100132707
LOC100134229
LOC100134713
LOC100287482
MOXD2P
ZNF783
MIR548F3
MIR548I4
MIR548F4
MIR548T
MTRNR2L6
MIR3907
MIR3666
LOC100505483
LOC100506585
LOC100507421
GIMAP1-GIMAP5
MIR4468

Genes in Wide Peak

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

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

Genes
BIRC3
ATM
CCND1
CBL
DDX6
DDX10
FLI1
MLL
NUMA1
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
hsa-mir-326
hsa-mir-139
hsa-mir-3165
hsa-mir-548k
hsa-mir-3164
ACAT1
ACRV1
BIRC2
APLP2
APOA1
APOA4
APOC3
ARCN1
PHOX2A
ARRB1
FXYD2
CXCR5
CAPN5
CASP1
CASP4
CASP5
SERPINH1
CD3D
CD3E
CD3G
CTSC
CHEK1
CLNS1A
CPT1A
CRYAB
DHCR7
DLAT
DLG2
DPAGT1
DRD2
CTTN
ETS1
FDX1
FGF3
FGF4
FOLR1
FOLR2
FOLR3
FUT4
SLC37A4
LRRC32
GRIA4
GRIK4
GRM5
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IGHMBP2
IL10RA
IL18
INPPL1
STT3A
KCNJ1
KCNJ5
KRTAP5-9
VWA5A
MAP6
MCAM
MMP1
MMP3
MMP7
MMP8
MMP10
MMP12
MMP13
MRE11A
MTNR1B
MYO7A
NCAM1
NDUFC2
NFRKB
NNMT
NPAT
NRGN
OMP
OPCML
P2RY2
P2RY6
PAK1
PDE2A
PGR
PPP2R1B
PRCP
PRKRIR
PTS
PVRL1
RAB6A
RDX
SNORD15A
RPS3
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
THRSP
THY1
TRPC6
TYR
UCP2
UCP3
UPK2
UVRAG
WNT11
ZBTB16
ZNF202
CUL5
FZD4
PPFIA1
BARX2
OR7E2P
JRKL
EED
FADD
ZNF259
MTMR2
USP2
HTR3B
ZW10
MMP20
UBE4A
MED17
EI24
MTL5
FEZ1
CEP57
ARHGAP32
SPCS2
ARHGEF17
GAB2
C2CD2L
FCHSD2
FGF19
NAALAD2
KCNE3
IL18BP
RBM7
MPZL2
YAP1
HYOU1
ATP5L
POLD3
STARD10
NEU3
ME3
GPR83
SRSF8
ADAMTS8
PRSS23
TREH
SLCO2B1
CEP164
SHANK2
IGSF9B
ENDOD1
EXPH5
PHLDB1
FAM168A
SIK2
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
RAB38
CADM1
PANX1
POU2F3
CHRDL2
C11orf51
TSKU
HINFP
REXO2
C2CD3
ODZ4
OR8G2
OR8B8
OR8G1
TIMM8B
MYEOV
OR8B2
CHORDC1
ACAD8
B3GAT1
RAB30
DCPS
C11orf54
C11orf67
ZBTB44
THYN1
DDX25
NOX4
NTM
CDON
GAL
SIDT2
CHCHD8
TRAPPC4
PPME1
C11orf73
CWC15
PCF11
MRPL48
RSF1
SPA17
FXYD6
CNTN5
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
SYTL2
ANKRD49
TTC12
LAMTOR1
ANO1
NADSYN1
FAM86C1
C11orf57
PPP6R3
RNF121
ACER3
ELMOD1
FOXRED1
KDM4D
SCN3B
VPS11
TMEM126B
TEX12
CRTAM
TMPRSS4
IFT46
C11orf75
C11orf30
PRDM10
TRIM49
DSCAML1
GRAMD1B
USP35
KIAA1377
ARHGAP20
USP28
KRTAP5-8
PLEKHB1
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
MOGAT2
PAAF1
PDGFD
TMPRSS5
GDPD5
CLPB
PUS3
MFRP
JAM3
BCO2
TMEM133
TMPRSS13
TMEM126A
DCUN1D5
KIAA1826
KIRREL3
DGAT2
BUD13
TMEM25
RPUSD4
TBRG1
RELT
UBASH3B
C11orf70
DIXDC1
KIAA1731
ZC3H12C
ATG16L2
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
INTS4
VPS26B
GLB1L3
SNORD15B
TIRAP
CARD16
C1QTNF5
TMEM123
PANX3
MRGPRD
APOA5
MRGPRF
ARAP1
SLC36A4
FAT3
TRIM64
TMEM45B
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
XRRA1
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
MRPL21
TPCN2
SPATA19
GDPD4
C11orf82
CCDC83
ORAOV1
LRTOMT
HEPACAM
OAF
FAM181B
CCDC89
DEFB108B
ANGPTL5
RNF169
ANKK1
RNF214
AQP11
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
P4HA3
PGM2L1
KLHL35
LOC283214
KCTD21
CCDC84
TMEM225
OR8D4
ANKRD42
C11orf53
LOC341056
OR2AT4
HEPHL1
C11orf34
DNAJB13
KRTAP5-10
LIPT2
VSTM5
GUCY2E
TRIM77P
FOLR4
KDM4DL
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
FLJ42102
LOC399939
LOC399940
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR139
MIR34B
MIR34C
DDI1
BLID
KRTAP5-7
KRTAP5-11
CARD17
LINC00167
MIR326
SCARNA9
HEPN1
TRIM64B
TRIM53P
TRIM49L2
UBTFL1
LOC643037
LOC643733
LOC643923
CLDN25
LOC649133
RPL23AP64
SNORA8
SNORA1
SNORA18
SNORA40
SNORA25
SNORA32
SNORD5
SNORD6
TRIM49L1
MIR708
LOC100128239
LOC100129216
LOC100132078
LOC100133315
PATE3
LOC100288077
LOC100288346
MIR1304
MIR548K
SNORA70E
BACE1-AS
MIR4300
MIR4301
MIR3167
MIR3165
MIR1260B
LOC100499227
MIR3920
MIR3656
MIR3664
LOC100506233
LOC100506368
CASP12
LOC100507050
LOC100507392
LOC100526771
HSPB2-C11orf52
NDUFC2-KCTD14
FXYD6-FXYD2
MIR4697
MIR4490
MIR4493
MIR4491
MIR4492
MIR4696
MIR4692
MIR4693
LOC100652768

Genes in Wide Peak

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

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

Genes
BRCA2
CDX2
ERCC5
FLT3
LCP1
RB1
LHFP
TTL
hsa-mir-1267
hsa-mir-4306
hsa-mir-623
hsa-mir-3170
hsa-mir-92a-1
hsa-mir-622
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
hsa-mir-2276
PARP4
ALOX5AP
ATP12A
ATP4B
ATP7B
KLF5
BTF3P11
CDK8
RCBTB2
CLN5
COL4A1
COL4A2
CPB2
DACH1
DCT
GPR183
EDNRB
EFNB2
ELF1
ESD
F7
F10
FGF9
FGF14
GPC5
FOXO1
FLT1
GAS6
GJA3
GJB2
GPR12
GPR18
MLNR
GTF2F2
GTF3A
GUCY1B2
HMGB1
HTR2A
ING1
PDX1
KPNA3
IPO5
LAMP1
LIG4
LMO7
MAB21L1
SMAD9
MIPEP
NEK3
PABPC3
PCCA
PCDH8
PCDH9
UBL3
POU4F1
DNAJC3
RAP2A
RFC3
RFXAP
GRK1
RNF6
RPL21
ATXN8OS
SGCG
SLC7A1
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
TPT1
TRPC4
TUBA3C
UCHL3
ZIC2
ZMYM2
IFT88
STK24
CUL4A
TNFSF11
IRS2
SCEL
SUCLA2
DLEU2
TSC22D1
PROZ
ARHGEF7
CDC16
CCNA1
CLDN10
MTMR6
DCLK1
ZMYM5
ITGBL1
KL
TM9SF2
ITM2B
MTRF1
UTP14C
NUPL1
TBC1D4
GPC6
FRY
MBNL2
FARP1
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
SPRY2
ABCC4
SAP18
DLEU1
TUBGCP3
N4BP2L2
PIBF1
OLFM4
POSTN
TNFSF13B
GJB6
HSPH1
WASF3
SUGT1
LECT1
SOX21
WBP4
AKAP11
KLF12
EXOSC8
RASA3
FNDC3A
DZIP1
DIS3
MYO16
PDS5B
MYCBP2
KIAA0564
ZC3H13
SPG20
LRCH1
ATP11A
MCF2L
MTUS2
DOCK9
TGDS
SLITRK5
FBXL3
SACS
INTS6
LATS2
CKAP2
NUFIP1
SNORD102
NBEA
OXGR1
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
CRYL1
PHF11
POMP
UFM1
ATP8A2
IL17D
NDFIP2
MPHOSPH8
BIVM
SOHLH2
TMCO3
ENOX1
ARGLU1
DCUN1D2
RCBTB1
PSPC1
NUDT15
KIAA1704
TNFRSF19
FAM48A
ANKRD10
RAB20
CARKD
UGGT2
PCID2
CENPJ
THSD1
RNF17
CYSLTR2
SPRYD7
COG6
KLHL1
RBM26
XPO4
PCDH20
UPF3A
MRP63
KDELC1
CARS2
RNF219
NAA16
RNASEH2B
DHRS12
GRTP1
BORA
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
SLITRK6
EBPL
TMTC4
C13orf33
ABHD13
ZIC5
A2LD1
KBTBD6
STARD13
N4BP2L1
TEX30
TPTE2
EPSTI1
ADPRHL1
SLITRK1
KCTD12
ARL11
WDFY2
CG030
TEX29
LINC00284
METTL21CP1
CSNK1A1L
RXFP2
TEX26
SLAIN1
PRR20A
SPACA7
RNF113B
LINC00410
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
GPR180
STOML3
COMMD6
CLYBL
METTL21C
EEF1DP3
FAM123A
USP12
MTIF3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
N6AMT2
SKA3
EFHA1
SPATA13
LNX2
SLC25A30
ZDHHC20
PAN3
NALCN
PHF2P1
HS6ST3
DAOA
DAOA-AS1
FGF14-IT1
LOC283481
LINC00346
CHAMP1
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
ANKRD20A9P
UBAC2
LINC00550
LINC00347
C1QTNF9
FREM2
NEK5
FAM70B
LINC00442
TPTE2P6
THSD1P1
KCTD4
RASL11A
C1QTNF9B
SHISA2
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
C13orf35
MIR15A
MIR16-1
MIR17
MIR18A
MIR19A
MIR19B1
MIR20A
MIR92A1
MIR17HG
ATP5EP2
LOC440131
ALG11
MZT1
C1QTNF9B-AS1
SNORA27
TSC22D1-AS1
MIR4500HG
FLJ44054
CCDC168
BASP1P1
TPTE2P1
PRHOXNB
ZAR1L
SERPINE3
CTAGE11P
FLJ41484
SNORA31
MIR621
MIR622
MIR623
LINC00460
FAM155A
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
ANKRD26P3
LINC00552
RPL21P28
FKSG29
LINC00426
TPT1-AS1
LINC00421
PAN3-AS1
UBAC2-AS1
MCF2L-AS1
MIR1297
MIR548F5
MIR759
MIR2276
MIR320D1
MIR4306
MIR3170
MIR4305
MIR3169
MIR3665
MIR3613
RBM26-AS1
LOC100506394
LINC00327
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
BIVM-ERCC5
MIR2681
MIR548AN
MIR4500
MIR4705
MIR4499
MIR4703
LOC100616668

Genes in Wide Peak

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

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

Genes
APC
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
hsa-mir-1244-2
hsa-mir-548f-3
ADRA1B
ADRB2
ANXA6
ATOX1
ALDH7A1
BNIP1
CAMK4
CAMK2A
CAMLG
CANX
CCNG1
CD14
CDC25C
CDO1
CDX1
AP3S1
CLTB
CSF1R
CSF2
CSNK1A1
CSNK1G3
NKX2-5
CTNNA1
DBN1
DMXL1
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EFNA5
EGR1
ETF1
F12
FABP6
FAT2
FBN2
FER
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
HSD17B4
HSPA4
HSPA9
NDST1
HTR4
IK
IL3
IL4
IL5
IL9
IL12B
IL13
IRF1
KCNMB1
KCNN2
LCP2
LECT2
LMNB1
LOX
LTC4S
SMAD5
MAN2A1
MCC
MFAP3
MGAT1
MSX2
NDUFA2
NEUROG1
NPY6R
PCDH1
PCDHGC3
PDE6A
PFDN1
PGGT1B
PITX1
POU4F3
PPIC
PPP2CA
PPP2R2B
MAPK9
PROP1
PURA
RARS
RPS14
SGCD
SKP1
SLC6A7
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SNCB
SNX2
SPARC
SPINK1
SPOCK1
SRP19
STK10
TAF7
TCF7
ZNF354A
TCOF1
TGFBI
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
REEP5
NME5
PDLIM4
STC2
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
ATP6V0E1
ATG12
PTTG1
PDLIM7
NREP
CNOT8
RAB9BP1
HAND1
MED7
MYOT
ADAMTS2
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
SNCAIP
CLINT1
PCDHGA8
PCDHA9
MATR3
MAML1
KIAA0141
JAKMIP2
PJA2
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
PPIP5K2
WWC1
FBXW11
ACSL6
PHF15
LARP1
HARS2
ZNF346
TNFAIP8
GEMIN5
PCDHGA12
LRRTM2
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
OR4F3
HAVCR1
SNORD63
SNORA74A
CYFIP2
PKD2L2
UQCRQ
AFF4
PRELID1
IL17B
MAT2B
SLC27A6
SNX24
MRPL22
PCDHB1
KCNIP1
ZNF354C
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
DCTN4
MZB1
PAIP2
CDKL3
PCDH12
FAM13B
FAM53C
REEP2
PRR16
COMMD10
DDX41
NOP16
LARS
CXXC5
HMP19
UIMC1
RAPGEF6
KDM3B
PHAX
RAB24
RBM27
NEURL1B
FLJ11235
FAM193B
PCDHB18
PCDHB17
TMED9
ZCCHC10
CDHR2
WDR55
ANKHD1
CCDC99
THG1L
TMCO6
TRIM36
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
FEM1C
C5orf15
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
ZNF608
KCTD16
SEMA6A
PCDHB16
HMHB1
C5orf54
EPB41L4A
SIL1
GMCL1P1
ARAP3
RMND5B
FBXL17
YTHDC2
GRAMD3
PCYOX1L
CCNJL
SH3TC2
PANK3
SAP30L
TXNDC15
BTNL8
DOK3
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
NUDT12
SLC4A9
SLC25A2
TSSK1B
PCDHB19P
PCBD2
PSD2
THOC3
C5orf32
MEGF10
SPINK7
TRIM52
HAVCR2
AGXT2L2
C5orf62
TSLP
FCHSD1
UNC5A
C5orf30
LYRM7
TRIM41
SLC25A46
BOD1
CDKN2AIPNL
COL23A1
TIMD4
ZNF300
MYOZ3
UBTD2
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
EPB41L4A-AS1
MARCH3
LEAP2
SCGB3A2
ZNF354B
C5orf47
PPARGC1B
PRRC1
C5orf58
ZNF474
OR2Y1
AFAP1L1
GRPEL2
LSM11
GPR151
STARD4
WDR36
ZNF300P1
NUDCD2
UBLCP1
SOWAHA
SHROOM1
C5orf24
C5orf20
SLC36A2
SPINK13
C5orf41
CEP120
SLC25A48
SRFBP1
LOC153469
ZMAT2
BTNL9
CCDC112
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
DCP2
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
LOC202181
STK32A
AQPEP
SLC36A1
EIF4E1B
RASGEF1C
LOC257358
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
DTWD2
RELL2
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
OR2V2
ZNF454
C5orf60
CHSY3
LOC340037
TMEM173
FAM170A
LOC340073
LOC340074
ARSI
PFN3
ZNF879
IRGM
FBLL1
CATSPER3
NIPAL4
TICAM2
DND1
C5orf25
FLJ38109
C5orf48
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
TMEM232
LOC643201
GRXCR2
SPINK9
ZFP62
LOC644100
FLJ33630
CCNI2
CBY3
FAM153C
SNORA13
SNORA74B
MIR585
SNHG4
MIR143HG
LOC728342
LOC728554
LOC729080
AACSP1
LOC729678
OR4F29
VTRNA2-1
MIR874
FAM196B
LOC100132062
LOC100132287
LOC100133331
C5orf52
LOC100268168
LOC100289673
MIR1289-2
MIR1229
MIR103B1
MIR1244-1
TMED7-TICAM2
MIR1244-3
MIR1244-2
MIR3142
MIR3141
MIR4281
MIR3655
MIR3912
MIR3936
MIR3661
LOC100505658
LOC100505678
LOC100505841
LOC100507387
MIR4633
MIR4634
MIR4461
MIR4460
MIR4638
MIR378E
LOC100859930

Arm-level results

Table 3. Get Full Table Arm-level significance table - 10 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.24 | 0.015 | 0.999 | 0.33 | 1.39 | 0.301
1q | 1955 | 0.21 | -0.397 | 0.999 | 0.32 | 1.25 | 0.302
2p | 924 | 0.18 | -0.951 | 0.999 | 0.31 | 0.928 | 0.471
2q | 1556 | 0.12 | -1.74 | 0.999 | 0.26 | 0.196 | 0.687
3p | 1062 | 0.08 | -2.43 | 0.999 | 0.29 | 0.588 | 0.506
3q | 1139 | 0.08 | -2.29 | 0.999 | 0.33 | 1.27 | 0.302
4p | 489 | 0.19 | -0.983 | 0.999 | 0.23 | -0.447 | 0.96
4q | 1049 | 0.15 | -1.45 | 0.999 | 0.26 | 0.178 | 0.687
5p | 270 | 0.29 | 0.449 | 0.999 | 0.18 | -1.14 | 0.96
5q | 1427 | 0.33 | 1.23 | 0.94 | 0.24 | -0.113 | 0.807
6p | 1173 | 0.26 | 0.209 | 0.999 | 0.24 | -0.0601 | 0.806
6q | 839 | 0.26 | 0.135 | 0.999 | 0.15 | -1.49 | 0.96
7p | 641 | 0.34 | 1.35 | 0.94 | 0.14 | -1.6 | 0.96
7q | 1277 | 0.30 | 0.908 | 0.999 | 0.16 | -1.27 | 0.96
8p | 580 | 0.25 | -0.0805 | 0.999 | 0.29 | 0.448 | 0.569
8q | 859 | 0.21 | -0.645 | 0.999 | 0.21 | -0.645 | 0.96
9p | 422 | 0.15 | -1.39 | 0.999 | 0.40 | 2.3 | 0.0429
9q | 1113 | 0.28 | 0.384 | 0.999 | 0.29 | 0.651 | 0.506
10p | 409 | 0.03 | -2.75 | 0.999 | 0.45 | 3.16 | 0.00458
10q | 1268 | 0.04 | -2.59 | 0.999 | 0.47 | 3.71 | 0.000835
11p | 862 | 0.11 | -1.76 | 0.999 | 0.49 | 3.84 | 0.000627
11q | 1515 | 0.09 | -1.97 | 0.999 | 0.41 | 2.68 | 0.0162
12p | 575 | 0.19 | -1.05 | 0.999 | 0.20 | -0.777 | 0.96
12q | 1447 | 0.10 | -2.25 | 0.999 | 0.21 | -0.582 | 0.96
13q | 654 | 0.00 | -2.98 | 0.999 | 0.50 | 4.06 | 0.000486
14q | 1341 | 0.23 | -0.259 | 0.999 | 0.47 | 3.44 | 0.00193
15q | 1355 | 0.21 | -0.587 | 0.999 | 0.30 | 0.768 | 0.506
16p | 872 | 0.28 | 0.338 | 0.999 | 0.29 | 0.603 | 0.506
16q | 702 | 0.15 | -1.17 | 0.999 | 0.54 | 4.58 | 9.35e-05
17p | 683 | 0.23 | -0.336 | 0.999 | 0.30 | 0.724 | 0.506
17q | 1592 | 0.16 | -1.29 | 0.999 | 0.18 | -1.01 | 0.96
18p | 143 | 0.21 | -0.71 | 0.999 | 0.32 | 0.861 | 0.486
18q | 446 | 0.22 | -0.571 | 0.999 | 0.34 | 1.27 | 0.302
19p | 995 | 0.33 | 1.19 | 0.94 | 0.16 | -1.24 | 0.96
19q | 1709 | 0.23 | -0.214 | 0.999 | 0.19 | -0.767 | 0.96
20p | 355 | 0.37 | 1.72 | 0.851 | 0.17 | -1.18 | 0.96
20q | 753 | 0.40 | 2.27 | 0.464 | 0.12 | -1.75 | 0.96
21q | 509 | 0.30 | 0.631 | 0.999 | 0.30 | 0.631 | 0.506
22q | 921 | 0.25 | -0.0154 | 0.999 | 0.45 | 3.11 | 0.00467
Xq | 1312 | 0.11 | -1.71 | 0.999 | 0.49 | 3.96 | 0.000502

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/3350407/GDAC_MergeDataFiles_3204382/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 52 Input Tumor Samples.

Tumor Sample Names
TCGA-DX-A1KU-01A-32D-A24M-01
TCGA-DX-A1KW-01A-22D-A24M-01
TCGA-DX-A1KX-01A-22D-A24M-01
TCGA-DX-A1KY-01A-11D-A24M-01
TCGA-DX-A1KZ-01A-11D-A24M-01
TCGA-DX-A1L0-01A-11D-A24M-01
TCGA-DX-A1L1-01A-11D-A24M-01
TCGA-DX-A1L2-01A-22D-A24M-01
TCGA-DX-A1L3-01A-11D-A24M-01
TCGA-DX-A2IZ-01A-11D-A21P-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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