Lung Squamous Cell Carcinoma: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.16a (cga svn revision 43808).

Summary

There were 289 tumor samples used in this analysis: 29 significant arm-level results, 29 significant focal amplifications, and 46 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 - 29 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
--- | --- | --- | --- | ---
3q26.33 | 4.119e-119 | 4.119e-119 | chr3:181227386-183901191 | 22
8p11.23 | 2.7142e-46 | 2.7142e-46 | chr8:38170522-38260814 | 2
11q13.3 | 6.4849e-36 | 6.4849e-36 | chr11:69617150-70248899 | 7
8q24.21 | 1.5646e-18 | 1.5646e-18 | chr8:128342867-128623910 | 2
2p16.1 | 8.0368e-12 | 8.0368e-12 | chr2:60529126-61154642 | 5
4q12 | 2.8041e-11 | 2.8041e-11 | chr4:56240288-56528782 | 5
7p11.2 | 3.8681e-10 | 3.8681e-10 | chr7:54767640-55798099 | 5
5p15.33 | 5.9247e-12 | 1.8848e-08 | chr5:1-4421494 | 38
19q13.2 | 3.6657e-12 | 8.4108e-06 | chr19:39592139-40024477 | 21
9p13.3 | 1.189e-06 | 1.7583e-05 | chr9:34197862-35921629 | 56
18q11.2 | 0.00014812 | 0.00014812 | chr18:23753292-24410984 | 4
1q21.2 | 0.00035208 | 0.00035208 | chr1:120523956-155972776 | 297
20q11.21 | 0.00060197 | 0.00060197 | chr20:26196264-30582729 | 26
14q13.3 | 0.0011129 | 0.0011129 | chr14:36782985-37620169 | 7
19q12 | 4.2976e-07 | 0.0011129 | chr19:28697976-30006956 | 4
2q31.2 | 0.0015243 | 0.0015243 | chr2:178083264-178126731 | 4
5p12 | 1.0569e-07 | 0.0023577 | chr5:30231933-50133343 | 89
17q25.1 | 0.0041419 | 0.0041419 | chr17:70568509-74432561 | 93
15q26.3 | 0.011135 | 0.011135 | chr15:89851677-102531392 | 93
12p13.33 | 0.011668 | 0.011668 | chr12:1-3480534 | 34
7q21.2 | 0.014772 | 0.014772 | chr7:91474555-93550446 | 25
6q12 | 0.020768 | 0.020768 | chr6:63667925-66482646 | 4
12q15 | 0.024745 | 0.024745 | chr12:67137789-71503288 | 29
22q11.21 | 0.052142 | 0.052142 | chr22:18613558-23816427 | 110
1p34.3 | 0.11154 | 0.11154 | chr1:39753329-40650788 | 18
3p11.1 | 0.11885 | 0.11885 | chr3:89652366-90236050 | 0 [EPHA3]
9p24.1 | 0.025859 | 0.12142 | chr9:5421313-5592144 | 3
18p11.32 | 0.16961 | 0.16961 | chr18:1-894241 | 10
21q21.1 | 0.17911 | 0.17911 | chr21:17519797-20410277 | 15

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.33.

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

Genes
SOX2
AP2M1
DVL3
EIF2B5
ABCC5
MCF2L2
ATP11B
LAMP3
DCUN1D1
KLHL24
PARL
YEATS2
MCCC1
MAP6D1
B3GNT5
KLHL6
HTR3C
HTR3D
HTR3E
SOX2-OT
FLJ46066
LOC100505687

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.23.

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

Genes
WHSC1L1
LETM2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11q13.3.

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

Genes
hsa-mir-548k
CTTN
FGF3
PPFIA1
FADD
ANO1
MIR548K

Genes in Wide Peak

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

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

Genes
POU5F1B
LOC727677

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 2p16.1.

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

Genes
REL
BCL11A
PAPOLG
FLJ16341
MIR4432

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q12.

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

Genes
CLOCK
NMU
TMEM165
PDCL2
LOC100506462

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7p11.2.

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

Genes
EGFR
SEC61G
LANCL2
VOPP1
FKBP9L

Genes in Wide Peak

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

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

Genes
hsa-mir-4277
NDUFS6
SDHA
SLC6A3
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
PP7080
IRX4
CEP72
AHRR
MRPL36
BRD9
IRX1
ZDHHC11
LPCAT1
CLPTM1L
NKD2
C5orf55
CCDC127
PLEKHG4B
C5orf38
IRX2
LOC285577
SLC6A19
SLC6A18
LRRC14B
SDHAP3
LOC728613
MIR4277
LOC100506688
MIR4457
MIR4456
MIR4635

Genes in Wide Peak

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

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

Genes
RPS16
SUPT5H
ZFP36
GMFG
PAK4
DLL3
PAF1
SAMD4B
MED29
LRFN1
PLEKHG2
TIMM50
EID2B
IL28A
IL28B
IL29
NCCRP1
SYCN
SELV
PAPL
MIR4530

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 9p13.3.

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

Genes
FANCG
NUDT2
CA9
CD72
CNTFR
GALT
IL11RA
NPR2
RMRP
CCL19
CCL21
TESK1
TLN1
TPM2
VCP
RGP1
RUSC2
SIGMAR1
CREB3
UNC13B
CCL27
DCTN3
KIAA1045
DNAJB5
SPAG8
DNAI1
SIT1
STOML2
UBAP1
TMEM8B
KIAA1161
GBA2
FAM214B
HINT2
C9orf24
PIGO
C9orf100
FP588
ARID3C
C9orf23
C9orf131
LOC158376
ATP8B5P
C9orf25
CCDC107
FAM205A
KIF24
ENHO
FAM205B
C9orf128
OR13J1
LOC415056
HRCT1
MSMP
FAM166B
MIR4667

Genes in Wide Peak

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

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

Genes
TAF4B
PSMA8
KCTD1
LOC728606

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q21.2.

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

Genes
ARNT
BCL9
MUC1
NOTCH2
TPM3
PDE4DIP
hsa-mir-555
hsa-mir-92b
hsa-mir-4258
hsa-mir-190b
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
ADAR
CHRNB2
CKS1B
CLK2
CTSK
CTSS
ECM1
EFNA1
EFNA3
EFNA4
ENSA
FCGR1A
FCGR1B
FDPS
FLG
FMO5
GBA
GBAP1
GJA5
GJA8
IL6R
ILF2
IVL
KCNN3
LOR
MCL1
SMCP
MTX1
NPR1
PDZK1
PI4KB
PKLR
PRKAB2
PSMB4
PSMD4
RAB13
RFX5
RIT1
RORC
RPS27
S100A1
S100A2
S100A3
S100A4
S100A5
S100A6
S100A7
S100A8
S100A9
S100A10
S100A11
S100A12
S100A13
SHC1
SPRR1A
SPRR1B
SPRR2A
SPRR2B
SPRR2C
SPRR2D
SPRR2E
SPRR2F
SPRR2G
SPRR3
VPS72
THBS3
TCHH
TUFT1
DAP3
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
ADAM15
PEX11B
SELENBP1
PRPF3
ARHGEF2
SEC22B
CHD1L
SETDB1
UBAP2L
SV2A
DENND4B
RBM8A
SCAMP3
SF3B4
PIAS3
HAX1
SEMA6C
POLR3C
TXNIP
PMVK
FAM189B
JTB
MTMR11
MLLT11
SLC27A3
TDRKH
CD160
CELF3
VPS45
KIAA0907
POGZ
SYT11
RPRD2
SNAPIN
RUSC1
CA14
NBPF14
C1orf43
CHTOP
LCE2B
SLC39A1
RNF115
TMOD4
CERS2
CRNN
BOLA1
ZBTB7B
APH1A
PLEKHO1
ACP6
GPR89B
OAZ3
DPM3
MRPS21
ADAMTSL4
CRCT1
GON4L
C1orf56
MSTO1
GOLPH3L
YY1AP1
UBE2Q1
FAM63A
ASH1L
LENEP
SLC50A1
CDC42SE1
OTUD7B
PGLYRP4
ATP8B2
FAM91A2
PBXIP1
S100A14
GATAD2B
CGN
ZNF687
HCN3
PRUNE
MRPL9
INTS3
SCNM1
TNFAIP8L2
C1orf54
TRIM46
TARS2
FLAD1
SNX27
ANP32E
HORMAD1
POLR3GL
LCE3D
AQP10
PYGO2
NUP210L
PGLYRP3
GNRHR2
THEM4
GABPB2
TCHHL1
RPTN
TDRD10
SHE
HIST2H3C
DCST2
LIX1L
S100A16
CREB3L4
C1orf51
HFE2
ANKRD35
LELP1
DCST1
BNIPL
SPRR4
PPIAL4A
PDIA3P
LCE4A
NBPF11
NUDT17
KRTCAP2
CRTC2
LCE5A
RIIAD1
THEM5
NBPF15
ANKRD34A
RUSC1-AS1
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
S100A7A
LINGO4
RXFP4
LCE1A
LCE1B
LCE1C
LCE1D
LCE1E
LCE1F
LCE2A
LCE2C
LCE2D
LCE3A
LCE3B
LCE3C
LCE3E
LOC375010
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
C1orf189
NBPF9
HIST2H2BF
KPRP
LCE6A
HIST2H4B
PRR9
PPIAL4G
PPIAL4D
LOC645166
LOC645676
POU5F1P4
S100A7L2
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
SCARNA4
SNORA42
MIR554
MIR555
MIR92B
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
MIR190B
C1orf68
MSTO2P
LOC100130000
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
LOC100289211
MIR4257
MIR4258
LOC100505666
TNFAIP8L2-SCNM1

Genes in Wide Peak

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

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

Genes
hsa-mir-3193
BCL2L1
FOXS1
ID1
TPX2
REM1
HM13
PDRG1
COX4I2
MYLK2
DEFB118
DUSP15
MLLT10P1
LINC00028
TTLL9
DEFB115
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
FRG1B
XKR7
PSIMCT-1
MIR3193

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q13.3.

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

Genes
NKX2-1
PAX9
NKX2-8
MBIP
SLC25A21
SFTA3
MIR4503

Genes in Wide Peak

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

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

Genes
UQCRFS1
LOC148145
LOC284395
LOC100505835

Genes in Wide Peak

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

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

Genes
NFE2L2
hsa-mir-3128
HNRNPA3
MIR3128

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5p12.

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

Genes
LIFR
hsa-mir-1274a
hsa-mir-580
hsa-mir-579
hsa-mir-4279
C6
C7
C9
CDH6
DAB2
FGF10
FYB
GDNF
GHR
HMGCS1
IL7R
NPR3
OXCT1
PRKAA1
PRLR
PTGER4
RAD1
RPL37
SEPP1
SKP2
SLC1A3
TARS
ZNF131
OSMR
NUP155
PAIP1
MRPS30
SUB1
PDZD2
NNT
TTC33
AMACR
NIPBL
RAI14
FBXO4
DROSHA
SLC45A2
RXFP3
ZFR
MTMR12
WDR70
BRIX1
C5orf22
CCL28
GOLPH3
C5orf28
AGXT2
C5orf42
PARP8
SPEF2
ADAMTS12
CARD6
LMBRD2
C1QTNF3
EMB
HEATR7B2
EGFLAM
NADKD1
UGT3A1
CAPSL
DNAJC21
TTC23L
LOC153684
UGT3A2
NIM1
RANBP3L
RICTOR
C5orf51
LOC340113
PLCXD3
HCN1
C5orf34
C5orf39
SNORD72
LOC646719
LOC648987
MIR580
CCDC152
LOC100132356
MIR4279
MIR3650
LOC100506548
C1QTNF3-AMACR
EGFLAM-AS4

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q25.1.

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

Genes
ACOX1
CDK3
EVPL
FDXR
FOXJ1
GALK1
GRB2
GRIN2C
H3F3B
ICT1
ITGB4
LLGL2
PRPSAP1
RPL38
SUMO2
SRP68
SSTR2
GALR2
SPHK1
SLC16A5
SLC9A3R1
COG1
RECQL5
KIAA0195
ATP5H
CD300C
CD300A
GGA3
EXOC7
KCTD2
WBP2
CDC42EP4
NAT9
SAP30BP
NT5C
CDR2L
MRPS7
HN1
SDK2
TMEM104
C17orf80
GPRC5C
MIF4GD
CASKIN2
SLC25A19
UBE2O
DNAI2
MRPL38
ARMC7
NUP85
MYO15B
QRICH2
FAM104A
MGC16275
FBF1
UNK
TRIM47
OTOP2
TTYH2
RNF157
USH1G
CD300LB
KIF19
CD300LF
C17orf77
SLC39A11
TRIM65
UNC13D
LINC00469
FADS6
C17orf28
TSEN54
FAM100B
RAB37
CD300E
OTOP3
GPR142
ZACN
BTBD17
LINC00511
LOC400620
CPSF4L
C17orf109
C17orf110
CD300LD
TEN1
LOC100287042
LOC100499467
MIR3678
MIR3615
LOC100507218
TEN1-CDK3
MIR4738

Genes in Wide Peak

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

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

Genes
BLM
IDH2
CRTC3
hsa-mir-1302-10
hsa-mir-1469
hsa-mir-3175
hsa-mir-3174
hsa-mir-9-3
ALDH1A3
ANPEP
CHD2
FES
IGF1R
MAN2A2
MEF2A
FURIN
PCSK6
PLIN1
POLG
SNRPA1
NR2F2
ST8SIA2
PEX11A
IQGAP1
PRC1
SV2B
AP3S2
SEMA4B
CIB1
CHSY1
SYNM
GABARAPL3
VPS33B
OR4F4
SLCO3A1
NGRN
RHCG
LINS
FANCI
MCTP2
SELS
MESP1
UNC45A
RGMA
WDR93
TTC23
LRRK1
TM2D3
C15orf42
RCCD1
ARRDC4
LOC91948
TARSL2
LRRC28
ASB7
LYSMD4
PGPEP1L
LOC145820
C15orf32
MESP2
SPATA8
ADAMTS17
DNM1P46
CERS3
LOC254559
LOC283761
FAM169B
ZNF774
C15orf38
KIF7
ZNF710
HDDC3
WASH3P
FLJ42289
C15orf58
OR4F6
OR4F15
FAM174B
LOC400456
MIR9-3
TTLL13
ASB9P1
FAM138E
LOC100144604
GPCRLTM7
DDX11L1
DDX11L9
MIR1469
MIR3175
LOC100507217
LOC100507472
C15orf38-AP3S2
MIR4714

Genes in Wide Peak

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

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

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

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 7q21.2.

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

Genes
CDK6
AKAP9
hsa-mir-489
hsa-mir-1285-1
CALCR
KRIT1
CYP51A1
GNGT1
PEX1
MTERF
TFPI2
ANKIB1
SAMD9
CCDC132
GATAD1
RBM48
MGC16142
SAMD9L
HEPACAM2
FAM133B
LRRD1
MIR489
MIR653
LOC728066
MIR4652

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q12.

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

Genes
PTP4A1
PHF3
LGSN
EYS

Genes in Wide Peak

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

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

Genes
MDM2
hsa-mir-1279
CPM
IFNG
LYZ
CNOT2
PTPRB
PTPRR
RAP1B
YEATS4
DYRK2
CCT2
FRS2
CPSF6
KCNMB4
IL22
SLC35E3
IL26
CAND1
MDM1
NUP107
RAB3IP
BEST3
LRRC10
MIR1279
SNORA70G
MIR3913-2
MIR3913-1
LOC100507250

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 22q11.21.

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

Genes
BCR
CLTCL1
hsa-mir-650
hsa-mir-130b
hsa-mir-649
hsa-mir-1286
hsa-mir-1306
hsa-mir-185
ARVCF
COMT
CRKL
GGT3P
GNAZ
GP1BB
GSC2
SERPIND1
PI4KA
SEPT5
MAPK1
PRODH
RANBP1
SLC7A4
SLC25A1
TBX1
CLDN5
HIRA
UBE2L3
UFD1L
VPREB1
ZNF74
DGCR6
LZTR1
DGCR14
CDC45
TOP3B
P2RX6
SNAP29
RAB36
PPM1F
DGCR2
TXNRD2
USP18
HIC2
PRAME
TSSK2
SDF2L1
PPIL2
DGCR11
DGCR9
POM121L1P
DGCR5
DGCR10
FBXW4P1
TRMT2A
RTDR1
POM121L8P
YPEL1
ZDHHC8
MED15
TUBA8
DGCR8
GNB1L
MRPL40
RTN4R
C22orf29
THAP7
TMEM191A
KLHL22
DGCR6L
RIMBP3
SCARF2
GGTLC2
LOC96610
MGC16703
C22orf39
C22orf25
ZNF280A
ZNF280B
LOC150185
LOC150197
AIFM3
RIMBP3C
YDJC
ZDHHC8P1
CCDC116
POM121L4P
LOC284865
PI4KAP2
LOC388849
LOC400891
BCRP2
MIR130B
MIR185
THAP7-AS1
P2RX6P
RIMBP3B
TMEM191C
LOC648691
CES5AP1
MIR650
TMEM191B
PI4KAP1
LOC729444
MIR301B
MIR1286
MIR1306
IGLL5
MIR3618
SEPT5-GP1BB
MIR4761

Genes in Wide Peak

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

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

Genes
MYCL1
BMP8B
PPT1
RLF
PABPC4
PPIE
CAP1
MACF1
HEYL
HPCAL4
TRIT1
OXCT2
NT5C1A
MFSD2A
BMP8A
KIAA0754
SNORA55
PPIEL

Genes in Wide Peak

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

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

Genes
CD274
C9orf46
PDCD1LG2

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18p11.32.

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

Genes
CETN1
TYMS
YES1
USP14
THOC1
CLUL1
ENOSF1
COLEC12
C18orf56
ROCK1P1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 21q21.1.

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

Genes
hsa-mir-548x
hsa-mir-125b-2
hsa-let-7c
CXADR
TMPRSS15
BTG3
CHODL-AS1
C21orf91
CHODL
C21orf91-OT1
LINC00478
MIRLET7C
MIR125B2
MIR99A
C21orf37

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 - 46 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 | 3.6966e-103 | 7.971e-90 | chr9:21865498-21997722 | 2
8p23.2 | 5.3351e-45 | 5.3351e-45 | chr8:2079140-6262191 | 1
2q22.1 | 2.5084e-30 | 3.2962e-26 | chr2:139655617-143637838 | 1
10q23.31 | 2.1286e-19 | 2.1286e-19 | chr10:89617158-90034038 | 2
5q11.2 | 1.0599e-13 | 1.0599e-13 | chr5:58260298-59787985 | 3
3p25.3 | 2.3518e-09 | 7.1132e-08 | chr3:11593014-11833472 | 1
11p15.5 | 2.7811e-07 | 2.7605e-07 | chr11:1-5153260 | 148
19p13.3 | 3.7433e-07 | 3.6407e-07 | chr19:1-1386003 | 56
1p13.1 | 8.6527e-09 | 9.0021e-07 | chr1:108505744-149881397 | 233
13q14.2 | 2.4014e-09 | 1.328e-06 | chr13:48833767-49064807 | 2
2q36.1 | 3.9308e-12 | 2.8835e-06 | chr2:208890253-243199373 | 306
4q22.1 | 2.95e-08 | 7.8385e-06 | chr4:90844993-93240505 | 1
4q34.3 | 3.7194e-14 | 1.0013e-05 | chr4:178911874-191154276 | 64
3p13 | 3.2987e-13 | 1.1319e-05 | chr3:70016017-71592506 | 3
Xq22.3 | 3.5547e-05 | 3.6912e-05 | chrX:107395766-108023686 | 3
3p12.3 | 9.3918e-14 | 5.4489e-05 | chr3:75363575-93777876 | 26
13q12.11 | 1.9789e-07 | 0.00012057 | chr13:1-23524878 | 28
18q23 | 0.00022775 | 0.00022793 | chr18:73139336-78077248 | 19
11q25 | 2.0919e-05 | 0.00051143 | chr11:126870419-135006516 | 36
9p13.1 | 3.9535e-07 | 0.0020878 | chr9:38619152-71152237 | 50
16p13.3 | 0.0020347 | 0.0020878 | chr16:1-7388343 | 227
15q12 | 0.0022217 | 0.0021346 | chr15:1-44024489 | 300
21q21.1 | 0.0011319 | 0.0023132 | chr21:1-22117102 | 39
19q13.33 | 0.0028383 | 0.002886 | chr19:46970534-55970647 | 435
10p15.3 | 1.535e-05 | 0.002955 | chr10:1-1040137 | 5
14q11.2 | 0.0040094 | 0.003853 | chr14:1-23347553 | 78
1p36.32 | 4.3388e-05 | 0.0054093 | chr1:1-31345223 | 493
16q23.1 | 0.0074958 | 0.0073807 | chr16:78016120-79627770 | 2
22q11.21 | 0.0079043 | 0.0079043 | chr22:1-22096801 | 116
6q26 | 0.010181 | 0.010671 | chr6:161693099-163153207 | 1
7q36.1 | 0.0057075 | 0.010758 | chr7:120935777-159138663 | 332
Xp11.3 | 0.0045827 | 0.016318 | chrX:44702452-45008304 | 2
7q11.22 | 0.009837 | 0.017915 | chr7:66780207-70601215 | 1
9p21.2 | 6.6108e-18 | 0.017915 | chr9:27572512-28982153 | 4
17q25.3 | 0.013717 | 0.023083 | chr17:80031841-81195210 | 22
17q11.2 | 0.011177 | 0.028657 | chr17:29326736-29722618 | 5
4q32.2 | 1.7385e-06 | 0.030461 | chr4:156874529-186507186 | 113
10p15.1 | 0.000582 | 0.041381 | chr10:5018825-5136914 | 1
9p24.1 | 4.1384e-08 | 0.047317 | chr9:7799607-12693402 | 1
21q22.3 | 0.039082 | 0.072179 | chr21:35286767-45721071 | 104
Xp21.1 | 0.0060024 | 0.08032 | chrX:30865118-34644819 | 4
12q24.32 | 0.1187 | 0.12072 | chr12:72426099-133851895 | 445
Xp22.2 | 0.060599 | 0.13464 | chrX:1-12869983 | 59
6p25.2 | 0.15345 | 0.15384 | chr6:1-62234532 | 703
4p15.2 | 0.15884 | 0.16159 | chr4:1-52714468 | 275
11q22.1 | 0.016136 | 0.23068 | chr11:90601742-135006516 | 363

Genes in Wide Peak

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

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

Genes
CDKN2A
C9orf53

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p23.2.

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

Genes
CSMD1

Genes in Wide Peak

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

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

Genes
LRP1B

Genes in Wide Peak

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

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

Genes
PTEN
KLLN

Genes in Wide Peak

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

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

Genes
hsa-mir-582
PDE4D
PART1

Genes in Wide Peak

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

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

Genes
VGLL4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11p15.5.

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

Genes
CARS
HRAS
NUP98
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
AP2A2
RHOG
ART1
ASCL2
CD81
CD151
CDKN1C
CTSD
DRD4
DUSP8
IGF2
INS
IRF7
KCNQ1
LSP1
MUC2
MUC6
NAP1L4
SLC22A18
SLC22A18AS
POLR2L
PSMD13
RNH1
MRPL23
RPLP2
RRM1
SCT
TRIM21
STIM1
TALDO1
TH
TSPAN4
TNNI2
TNNT3
TRPC2
PHLDA2
ZNF195
RASSF7
IFITM1
BRSK2
TSPAN32
TSSC4
IFITM3
DEAF1
IFITM2
OR7E12P
KCNQ1OT1
PKP3
SIRT3
PGAP2
C11orf21
TRPM5
IGF2-AS1
BET1L
CEND1
CDHR5
TOLLIP
TRIM68
PIDD
KCNQ1DN
MMP26
CHRNA10
PNPLA2
PHRF1
SIGIRR
RIC8A
EPS8L2
CHID1
OR51G1
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
MOB2
SYT8
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR52B4
C11orf40
OR52I2
OR51E1
LOC143666
SCGB1C1
NLRP6
NS3BP
LOC255512
C11orf35
OR51F1
H19
EFCAB4A
TMEM80
C11orf36
ANO9
LOC338651
B4GALNT4
PDDC1
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR52K1
OR52I1
OR51D1
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
MIR483
SNORA52
LOC650368
LOC653486
SNORA54
INS-IGF2
MUC5B
MIR675
FAM99B
LOC100133161
MRPL23-AS1
MIR4298
MIR210HG
MIR4686
MIR4687

Genes in Wide Peak

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

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

Genes
STK11
FSTL3
hsa-mir-3187
hsa-mir-1302-11
ATP5D
AZU1
HCN2
BSG
CDC34
CIRBP
CNN2
CFD
ARID3A
EFNA2
ELANE
GPX4
GZMM
PALM
POLR2E
POLRMT
PRTN3
PTBP1
MADCAM1
PPAP2C
MED16
ABCA7
SBNO2
HMHA1
SHC2
FGF22
THEG
MIER2
C19orf24
RNF126
WDR18
LPPR3
OR4F17
KISS1R
MUM1
MIDN
R3HDM4
C19orf6
TPGS1
GRIN3B
C19orf21
C2CD4C
CIRBP-AS1
C19orf26
ODF3L2
WASH5P
FLJ45445
PRSS57
FAM138F
FAM138A
MIR3187
MIR4745

Genes in Wide Peak

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

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

Genes
BCL9
NOTCH2
NRAS
PDE4DIP
TRIM33
RBM15
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
ADORA3
ALX3
AMPD1
AMPD2
RHOC
ATP1A1
ATP5F1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CSF1
CELSR2
FCGR1A
FCGR1B
FMO5
GJA5
GJA8
GNAI3
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
HMGCS2
HSD3B1
HSD3B2
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PDZK1
PRKAB2
PSMA5
PTGFRN
RAP1A
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TSHB
WNT2B
CSDE1
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
TTF2
ITGA10
PEX11B
SLC16A4
CD101
SEC22B
CHD1L
LRIG2
RBM8A
TSPAN2
BCAS2
WARS2
CEPT1
PIAS3
HBXIP
POLR3C
TXNIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
ADAM30
CD160
DDX20
WDR47
CLCC1
NBPF14
PTPN22
PHGDH
CHIA
RNF115
GPSM2
SLC25A24
BOLA1
HAO2
ACP6
GPR89B
RSBN1
GDAP2
FAM46C
ST7L
PRPF38B
SLC22A15
LRIF1
CTTNBP2NL
FAM212B
TMEM167B
OLFML3
FAM91A2
AMIGO1
KIAA1324
DCLRE1B
WDR77
EPS8L3
VTCN1
DENND2D
SIKE1
TRIM45
VANGL1
GPR61
REG4
POLR3GL
PROK1
PSRC1
ATP1A1OS
FAM40A
ZNF697
HENMT1
GNRHR2
MAB21L3
HIST2H3C
ATXN7L2
C1orf194
LIX1L
HSD3BP4
DRAM2
C1orf88
C1orf162
SYT6
NBPF4
HFE2
ANKRD35
RP11-165H20.1
DENND2C
FNDC7
PPIAL4A
UBL4B
PDIA3P
NBPF11
NUDT17
SPAG17
HIPK1
AKR7A2P1
AKNAD1
MAGI3
FAM19A3
NBPF15
FAM102B
SYPL2
CYB561D1
ANKRD34A
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BC
HIST2H2BA
MYBPHL
NBPF7
LOC375010
SLC6A17
NOTCH2NL
FLJ39739
LOC388692
NBPF9
MIR197
LOC440600
BCL2L15
HIST2H2BF
PGCP1
HIST2H4B
SRG7
CYMP
LOC643441
LOC644242
PPIAL4G
PPIAL4D
LOC645166
EMBP1
SRGAP2P2
NBPF6
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
SCARNA2
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
MIR942
LOC100129269
LOC100130000
NBPF10
FCGR1C
LOC100286793
LOC100287722
LOC100289211
MIR320B1
MIR4256
LOC100506343

Genes in Wide Peak

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

Table S38. 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 2q36.1.

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

Genes
ATIC
ACSL3
IDH1
PAX3
FEV
hsa-mir-3133
hsa-mir-149
hsa-mir-4269
hsa-mir-562
hsa-mir-1471
hsa-mir-1244-1
hsa-mir-4268
hsa-mir-3132
hsa-mir-153-1
hsa-mir-3131
hsa-mir-26b
hsa-mir-548f-2
AAMP
ACADL
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CPS1
CRYBA2
CRYGA
CRYGB
CRYGC
CRYGD
CYP27A1
DES
DTYMK
EPHA4
ERBB4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
MAP2
MYL1
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTH2R
PTMA
PTPRN
SNORD20
RPE
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
XRCC5
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
LANCL1
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
CPS1-IT1
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ACCN4
DOCK10
MREG
PECR
C2orf83
MFF
CXCR7
RNPEPL1
MARCH4
WDFY1
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
PKI55
C2orf67
LOC151171
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
PIKFYVE
TIGD1
LOC200772
CCDC108
C2orf72
CXXC11
UNC80
RUFY4
DUSP28
ESPNL
ECEL1P2
LOC348761
C2orf62
RBM44
AQP12A
KLHL30
C2orf80
RESP18
C2orf82
OR6B2
ASB18
FLJ43879
VWC2L
MIR149
MIR153-1
MIR26B
DNAJB3
MIR375
LOC643387
PRR21
LOC646324
LOC646736
PRSS56
AQP12B
SNORA75
SCARNA6
SCARNA5
D2HGDH
LOC728323
DIRC3
LOC100129175
PP14571
LOC100130451
LOC100286922
MIR1471
MIR1244-1
MIR548F2
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3132
MIR4269
LOC100507443
UBE2F-SCLY
MIR4439
MIR4776-1
MIR4777
MIR2467
MIR4440
MIR4786
MIR4776-2
MIR4441

Genes in Wide Peak

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

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

Genes
FAM190A

Genes in Wide Peak

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

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

Genes
DUX4
hsa-mir-1305
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
HSP90AA4P
ING2
IRF2
KLKB1
MTNR1A
TLR3
SORBS2
FAM149A
DUX2
PDLIM3
CLDN22
UFSP2
CDKN2AIP
ODZ3
LRP2BP
STOX2
KIAA1430
TRAPPC11
MLF1IP
WWC2
SNX25
MGC45800
ZFP42
ENPP6
C4orf38
RWDD4
CCDC111
TRIML2
CCDC110
CYP4V2
LOC285441
LOC339975
TRIML1
ANKRD37
LOC389247
HELT
LOC401164
FAM92A3
C4orf47
DUX4L4
FRG2
SLED1
FLJ38576
DUX4L6
DUX4L5
DUX4L3
LINC00290
LOC728175
DUX4L2
LOC731424
CLDN24
LOC100288255
MIR1305
MIR3945
LOC100506229

Genes in Wide Peak

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

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

Genes
FOXP1
hsa-mir-1284
MIR1284

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq22.3.

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

Genes
COL4A5
COL4A6
IRS4

Genes in Wide Peak

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

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

Genes
hsa-mir-4273
hsa-mir-1324
EPHA3
GBE1
HTR1F
POU1F1
PROS1
ROBO1
ROBO2
CGGBP1
CHMP2B
ZNF654
ARL13B
CADM2
C3orf38
VGLL3
LOC401074
STX19
LOC440970
FLJ20518
FAM86DP
ZNF717
FRG2C
MIR1324
MIR4273
MIR4795

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 13q12.11.

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

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

Genes in Wide Peak

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

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

Genes
GALR1
MBP
NFATC1
ZNF236
CTDP1
ZNF516
TXNL4A
ADNP2
KCNG2
SALL3
RBFA
PQLC1
PARD6G
LOC284276
LOC339298
ATP9B
HSBP1L1
LOC100130522
LOC100131655

Genes in Wide Peak

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

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

Genes
FLI1
APLP2
ETS1
KCNJ1
KCNJ5
NFRKB
OPCML
ST14
BARX2
ARHGAP32
ADAMTS8
IGSF9B
NCAPD3
ACAD8
B3GAT1
ZBTB44
THYN1
NTM
PRDM10
TP53AIP1
JAM3
GLB1L2
VPS26B
GLB1L3
TMEM45B
ADAMTS15
C11orf45
SPATA19
KIRREL3-AS3
LOC283174
LOC283177
SNX19
LINC00167
LOC100128239
LOC100507392
MIR4697

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p13.1.

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

Genes
hsa-mir-1299
PGM5
ZNF658
FAM75A7
CNTNAP3
ANKRD20A1
FAM201A
CBWD5
LOC286297
FOXD4L3
FOXD4L4
AQP7P1
KGFLP1
FAM75A6
MGC21881
FAM74A1
FAM74A4
ZNF658B
LOC440896
ANKRD20A3
ANKRD20A2
AQP7P3
LOC442421
CBWD3
FAM27A
LOC572558
PGM5P2
LOC642236
FAM75A2
FAM75A4
LOC642929
LOC643648
CBWD6
FAM75A1
FAM74A2
FOXD4L6
FOXD4L5
LOC653501
KGFLP2
FAM75A3
FAM75A5
FAM74A3
CNTNAP3B
ANKRD20A4
FOXD4L2
LOC100132352
FAM27C
FAM95B1
FAM27B
LOC100133920

Genes in Wide Peak

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

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

Genes
CREBBP
TSC2
hsa-mir-3178
hsa-mir-940
hsa-mir-1225
hsa-mir-3177
hsa-mir-662
hsa-mir-3176
ABCA3
ADCY9
ARHGDIG
ATP6V0C
CCNF
CLCN7
ECI1
DNASE1
DNASE1L2
E4F1
GFER
HAGH
HBA1
HBA2
HBM
HBQ1
HBZ
HMOX2
IGFALS
MEFV
MPG
NDUFB10
NME3
NME4
NTHL1
NTN3
OR1F1
OR2C1
PDPK1
PKD1
PPL
RPL3L
RPS2
SRL
SOLH
SSTR5
TCEB2
TFAP4
TPSAB1
UBE2I
ZNF75A
ZNF174
ZNF200
ZNF205
ZNF213
NPRL3
AXIN1
RGS11
CACNA1H
BAIAP3
RHBDL1
CLDN6
CLDN9
PKMYT1
PIGQ
DNAJA3
SYNGR3
IL32
SLC9A3R2
SEC14L5
RAB11FIP3
IFT140
TELO2
NUBP2
ZNF263
TRAP1
MSLN
STUB1
MRPL28
TBL3
RNPS1
PRSS21
CLUAP1
MAPK8IP3
MGRN1
TPSD1
SRRM2
TPSG1
RAB26
ZNF500
DECR2
OR1F2P
SNORA64
SNORD60
UBN1
C16orf5
SOX8
AMDHD2
PAM16
NAGPA
TNFRSF12A
POLR3K
SEPX1
GNG13
KCTD5
ZNF434
HCFC1R1
LUC7L
ALG1
NMRAL1
TBC1D24
CASKIN1
CRAMP1L
RAB40C
TMEM8A
CHTF18
PRSS22
MLST8
RHBDF1
MMP25
NARFL
LINC00235
TPSB2
HS3ST6
PDIA2
UNKL
LINC00254
LMF1
FAM173A
MRPS34
METRN
THOC6
KREMEN2
CORO7
SNRNP25
ROGDI
TMEM204
NAA60
C16orf59
MGC3771
FAHD1
PRSS27
ITFG3
WDR24
TRAF7
FLYWCH1
HAGHL
NUDT16L1
C16orf13
FAM195A
SLX4
GNPTG
GLYR1
GLIS2
ZSCAN10
RHOT2
ZNF598
HN1L
SPSB3
TIGD7
RPUSD1
FLYWCH2
VASN
C16orf42
WFIKKN1
NOXO1
CCDC78
ZG16B
PRSS30P
PAQR4
ANKS3
FAM100A
SEPT12
RNF151
C16orf11
FBXL16
LOC146336
ZNF597
CCDC64B
C16orf89
C16orf71
FAM86A
WDR90
EME2
NLRC3
C16orf73
PRSS33
NPW
C16orf79
PGP
LINC00514
FLJ39639
NHLRC4
C16orf91
JMJD8
C16orf96
PRSS41
PRR25
C1QTNF8
PTX4
MSLNL
LOC440335
SNORA10
FLJ42627
CCDC154
C16orf90
ABCA17P
LOC652276
SNORA78
MIR662
SNHG9
CEMP1
MIR940
LOC100128788
LOC100134368
MIR1225
DDX11L10
MIR3178
MIR3177
MIR3176
MTRNR2L4
MIR3677
MIR3180-5
ERVK13-1
LOC100507501
LOC100507589
CORO7-PAM16
MIR4717
MIR4516

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q12.

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

Genes
BUB1B
C15orf55
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
APBA2
NBEAP1
CAPN3
CHRM5
CHRNA7
CKMT1B
EPB42
GABRA5
GABRB3
GABRG3
GANC
GCHFR
IPW
ITPKA
IVD
LTK
MAP1A
MEIS2
TRPM1
NDN
OCA2
PLCB2
RAD51
RYR3
SCG5
SNRPN
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
PAR5
JMJD7-PLA2G4B
SNAP23
HERC2
SNURF
TGM5
PPIP5K1
AQR
ARHGAP11A
LCMT2
SLC12A6
RASGRP1
GPR176
CHP
OIP5
BAHD1
FAN1
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
VPS39
FAM189A1
CCNDBP1
C15orf2
TMEM87A
RPAP1
DKFZP434L187
GREM1
RPUSD2
TUBGCP4
EHD4
NDUFAF1
NUSAP1
TMEM85
SPTBN5
KLF13
MAGEL2
DLL4
INO80
PPP1R14D
MTMR10
ZNF770
HAUS2
FAM82A2
DNAJC17
NOP10
NDNL2
C15orf24
PAK6
CASC5
AVEN
ATP10A
GJD2
STARD9
VPS18
ZFP106
CHAC1
C15orf29
TMEM62
NIPA2
C15orf41
ZFYVE19
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SNORD107
CHST14
TUBGCP5
TGM7
CATSPER2
NIPA1
PLA2G4E
PAR1
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
UBR1
LPCAT4
PLA2G4F
LRRC57
LOC283683
OR4N4
LOC283710
FAM98B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
FMN1
SNORD64
PAR4
PAR-SN
LOC348120
MRPL42P5
C15orf52
GOLGA8E
OR4M2
OR4N3P
HERC2P2
C15orf53
C15orf54
MIR211
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
LOC503519
CKMT1A
C15orf62
C15orf56
PHGR1
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
MIR626
MIR627
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727924
OIP5-AS1
GOLGA8C
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
LOC100128714
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
GOLGA8DP
JMJD7
PLA2G4B
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4509-3
MIR4715
TMCO5B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q21.1.

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

Genes
hsa-mir-548x
hsa-mir-125b-2
hsa-let-7c
hsa-mir-3118-5
hsa-mir-3156-3
BAGE
CXADR
TMPRSS15
HSPA13
TPTE
NRIP1
BTG3
USP25
RBM11
CHODL-AS1
C21orf15
C21orf91
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
CHODL
ANKRD30BP2
LIPI
ABCC13
C21orf91-OT1
POTED
LOC388813
LINC00478
ANKRD20A11P
MIRLET7C
MIR125B2
MIR99A
TEKT4P2
MIR3156-3
MIR3687
MIR3648
C21orf37

Genes in Wide Peak

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

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

Genes
KLK2
PPP2R1A
TFPT
ZNF331
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
AP2A1
KLK3
BAX
BCAT2
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CGB
AP2S1
CRX
DBP
EMP3
ETFB
FCAR
FCGRT
FLT3LG
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GPR32
GRIN2D
ARHGAP35
GYS1
HAS1
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LHB
LIG1
LIM2
MYBPC2
NDUFA3
NKG7
CNOT3
NPAS1
NTF4
NUCB1
POLD1
PRKCG
PRRG2
KLK7
KLK6
KLK10
PTGIR
PTPRH
RPL18
RPL28
RPS9
RPS11
RRAS
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SPIB
SULT2B1
SULT2A1
SYT5
TNNI3
TNNT1
TULP2
NR1H2
ZNF28
ZNF137P
ZNF175
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
CYTH2
NCR1
NAPSA
KLK4
ZNF432
DHX34
SAE1
LILRB2
RUVBL2
LILRB1
KDELR1
LILRB5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
KPTN
KLK8
PNKP
ATF5
PPP6R1
CARD8
ZC3H4
RPL13A
SYNGR4
LILRA4
NUP62
HSPBP1
PPP1R15A
KLK5
PRKD2
ZNF473
KLK13
CCDC9
PRPF31
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
SIGLEC7
BBC3
DKKL1
SIGLEC9
SIGLEC8
GPR77
DHDH
UBE2S
SLC6A16
STRN4
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
HSD17B14
GP6
VRK3
PTOV1
PPP1R12C
TRPM4
FAM83E
EPS8L1
RASIP1
TMEM160
PIH1D1
C19orf73
TMEM143
KLK15
NLRP2
ZNF701
ZNF83
ZNF415
CABP5
SPHK2
MEIS3
SLC17A7
RCN3
TTYH1
PNMAL2
PRR12
PLEKHA4
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ELSPBP1
LIN7B
ZNF649
TSEN34
MBOAT7
FKRP
LENG1
LILRP2
LILRA6
TBC1D17
MYH14
ZNF665
ZNF613
ZNF702P
ZNF614
FUZ
ZNF611
MED25
BCL2L12
GRWD1
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
SNORD35B
ZNF347
ZNF577
SUV420H2
C19orf48
SIGLEC10
SIGLEC12
KIR3DX1
ZNF616
ZNF766
ZNF468
ZNF160
CTU1
ZNF765
NLRP12
MYADM
ZNF845
CCDC114
ACPT
CGB5
CGB7
LRRC4B
LENG9
CGB8
GNG8
BIRC8
FAM71E1
RDH13
PTH2
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
KIR3DL3
CLDND2
ZNF816
COX6B2
OSCAR
ZNF813
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
TMEM190
TMC4
LOC147804
CCDC155
DACT3
CDC42EP5
ZNF836
ZNF610
ZNF600
ZNF320
ZNF114
ZNF525
SPACA4
NLRP7
C19orf76
TMEM86B
PRR24
NAPSB
IL4I1
TPRX1
MAMSTR
IZUMO1
C19orf63
MGC45922
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
VSTM1
TMEM150B
FAM71E2
VN1R2
VN1R4
C19orf81
ZNF677
C19orf51
LILRA5
ZNF808
ZNF761
TMEM238
ZNF321P
SIGLEC16
FLJ26850
ZNF880
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
TARM1
MIR371A
MIR372
MIR373
DPRX
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
SEC1
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR643
RPL13AP5
CEACAM18
SHISA7
FLJ30403
SIGLEC14
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
LOC100129083
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
ERVV-2
MIR1283-2
MIR1323
MIR1283-1
MIR3191
MIR3190
MIR320E
MIR4324
LOC100505681
LOC100505812
LOC100506012
LOC100506033
LOC100506068
LOC100507003
ZNF816-ZNF321P
MIR4752
MIR371B
MIR4749
MIR4750
MIR4751

Genes in Wide Peak

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

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

Genes
ZMYND11
DIP2C
LARP4B
TUBB8
C10orf108

Genes in Wide Peak

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

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

Genes
CCNB1IP1
hsa-mir-1201
ANG
APEX1
DAD1
HNRNPC
MMP14
PNP
OXA1L
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
SALL2
TEP1
SLC7A7
TOX4
PARP2
EDDM3A
SUPT16H
LRP10
OR10G3
OR10G2
OR4E2
SLC39A2
ZNF219
OSGEP
ARHGEF40
METTL3
RPGRIP1
NDRG2
CHD8
ABHD4
EDDM3B
METTL17
OR4K5
OR11H2
OR4K1
OR4K15
RNASE7
RAB2B
RPPH1
TMEM55B
TTC5
RNASE11
TPPP2
RNASE8
MRPL52
OR4K14
OR4L1
OR11H6
KLHL33
LOC283624
SNORD8
RNASE10
OR6S1
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
POTEG
OR11H12
RNASE13
OR4Q3
OR4M1
RNASE12
POTEM
LOC642426
ECRP
C14orf176
SNORD9
SNORD126

Genes in Wide Peak

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

Table S55. 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
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
ZBTB48
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MATN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SRSF4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
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
PTPRU
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
MECR
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
TMEM200B
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
LOC100129196
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
MIR4420
MIR4684
MIR4689
MIR4632
MIR4417
MIR378F
RCAN3AS

Genes in Wide Peak

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

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

Genes
CLEC3A
WWOX

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q11.21.

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q26.

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

Genes
PARK2

Genes in Wide Peak

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

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

Genes
BRAF
EZH2
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
CASP2
CDK5
CHRM2
CLCN1
CPA1
CPA2
DPP6
EN2
EPHA1
EPHB6
FLNC
GBX1
GPR37
GRM8
MNX1
HTR5A
IMPDH1
INSIG1
IRF5
KCNH2
KEL
LEP
MEST
MKLN1
NDUFA5
NDUFB2
NOS3
CNOT4
NRF1
PAX4
PIP
PODXL
PRSS1
PRSS2
TAS2R38
PTN
PTPRN2
PTPRZ1
RARRES2
RHEB
SHH
SLC4A2
SLC13A1
SMARCD3
SPAM1
AKR1D1
SSBP1
TBXAS1
UBE2H
VIPR2
XRCC2
ZYX
ARHGEF5
ZNF212
ZNF282
CUL1
TRIM24
MGAM
WASL
DGKI
ATP6V1F
ACCN3
PDIA4
UBE3C
FAM131B
FAM115A
DNAJB6
ABCF2
AASS
FAM3C
FASTK
ABCB8
PAXIP1
KLHDC10
SSPO
NUP205
AHCYL2
TNPO3
HYAL4
CLEC5A
MKRN1
POT1
CNTNAP2
HYALP1
GIMAP2
OR2F1
SLC13A4
COPG2
TPK1
SND1
SND1-IT1
DENND2A
ZNF777
TMEM176B
HIPK2
WDR91
REPIN1
HILPDA
FSCN3
ATP6V0A4
TAS2R3
TAS2R4
TAS2R16
CPA4
WNT16
PRKAG2
ZC3HC1
LUC7L2
MRPS33
NUB1
TAS2R5
CHPF2
NCAPG2
CHCHD3
WDR60
RBM28
TMEM140
GIMAP4
GIMAP5
TMEM176A
TRPV6
AGK
METTL2B
TRPV5
ZC3HAV1
AKR1B10
ACTR3B
KIAA1147
FAM40B
ESYT2
ZNF398
EXOC4
GALNT11
LRRC4
LMBR1
LINC00244
NOM1
CCDC136
PARP12
LRRC61
C7orf49
GCC1
ZNF767
TTC26
JHDM1D
TMUB1
SLC37A3
KRBA1
FAM71F1
SLC35B4
TMEM209
OR6W1P
ADCK2
PLXNA4
ZC3HAV1L
LOC93432
CADPS2
CPA5
CEP41
C7orf29
TSGA13
AGAP3
C7orf13
OR9A4
OR9A2
C7orf34
TMEM139
NOBOX
OR2A14
OR6B1
OR2F2
ZNF786
PRSS37
KLF14
C7orf45
SVOPL
MTPN
LRGUK
ASB10
PRSS58
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
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
LOC100505483
LOC100506585
LOC100507421
GIMAP1-GIMAP5
MIR4468

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp11.3.

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

Genes
KDM6A
DUSP21

Genes in Wide Peak

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

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

Genes
AUTS2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9p21.2.

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

Genes
hsa-mir-873
LINGO2
MIR876
MIR873

Genes in Wide Peak

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

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

Genes
CD7
CSNK1D
FASN
UTS2R
FOXK2
SECTM1
TBCD
SLC16A3
RAB40B
NARF
WDR45L
FN3K
C17orf62
FN3KRP
C17orf101
ZNF750
B3GNTL1
CCDC57
HEXDC
METRNL
FLJ43681
TEX19

Genes in Wide Peak

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

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

Genes
NF1
EVI2A
EVI2B
OMG
MIR4733

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q32.2.

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

Genes
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
hsa-mir-1979
AGA
SLC25A4
CASP3
CLCN3
CPE
DCTD
ETFDH
ACSL1
GK3P
GLRB
GPM6A
GRIA2
HMGB2
HPGD
ING2
IRF2
NEK1
NPY1R
NPY5R
PPID
MSMO1
TLL1
VEGFC
GLRA3
SAP30
HAND2
RAPGEF2
MFAP3L
ADAM29
ANXA10
KLHL2
SCRG1
PALLD
ANP32C
FBXO8
PDLIM3
SPOCK3
AADAT
FAM198B
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
SPATA4
ENPP6
ASB5
C4orf38
C4orf39
C4orf45
TRIM60
C4orf46
TMEM192
RWDD4
CCDC111
CCDC110
LOC285501
LOC340017
ANKRD37
LOC389247
TRIM61
HELT
FAM92A3
HSP90AA6P
C4orf47
GALNTL6
SLED1
MIR578
LINC00290
LOC728175
LOC731424
CLDN24
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 10p15.1.

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

Genes
AKR1C2

Genes in Wide Peak

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

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

Genes
PTPRD

Genes in Wide Peak

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

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

Genes
RUNX1
ERG
TMPRSS2
hsa-mir-3197
hsa-mir-802
AIRE
CBR1
CBR3
CBS
CRYAA
CSTB
DSCAM
RCAN1
DYRK1A
ETS2
HLCS
HMGN1
KCNE1
KCNJ6
KCNJ15
MX1
MX2
NDUFV3
PCP4
PDE9A
PKNOX1
PWP2
SH3BGR
SIM2
SLC5A3
TFF1
TFF2
TFF3
TRAPPC10
TTC3
U2AF1
WRB
CHAF1B
C21orf33
PDXK
RRP1
PSMG1
ABCG1
DOPEY2
KCNE2
DSCR4
DSCR3
B3GALT5
WDR4
HSF2BP
RRP1B
ICOSLG
MORC3
CLDN14
BACE2
C2CD2
DNMT3L
ZNF295
PIGP
UBASH3A
DSCR6
BRWD1
SLC37A1
LINC00160
FAM165B
LINC00112
LINC00111
SETD4
FAM3B
RIPK4
CLIC6
AGPAT3
PRDM15
TMPRSS3
MRPS6
RUNX1-IT1
DSCR8
RSPH1
UMODL1
LINC00310
LINC00313
C21orf88
LCA5L
IGSF5
SIK1
LINC00479
ZNF295-AS1
C21orf128
PLAC4
DSCR9
BRWD1-IT2
DSCR10
LINC00323
LINC00319
LOC284837
LINC00114
MIR802
LOC100133286
MIR3197
LOC100506334
LOC100506385
CBR3-AS1
DSCAM-AS1
MIR4760

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp21.1.

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

Genes
hsa-mir-548f-5
DMD
FTHL17
FAM47A

Genes in Wide Peak

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

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

Genes
ALDH2
BCL7A
BTG1
PTPN11
hsa-mir-4304
hsa-mir-1178
hsa-mir-620
hsa-mir-1302-1
hsa-mir-619
hsa-mir-1827
hsa-mir-4303
hsa-mir-135a-2
hsa-mir-1251
hsa-mir-331
hsa-mir-492
hsa-mir-618
hsa-mir-617
hsa-mir-1252
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
ATP2B1
SCARB1
CMKLR1
COX6A1
CRY1
CSRP2
DAO
DCN
EPYC
DTX1
DUSP6
EIF2B1
ELK3
STX2
GOLGA3
GTF2H3
HAL
HPD
IGF1
KCNC2
LTA4H
LUM
KITLG
MMP17
MSI1
MVK
MYBPC1
MYF5
MYF6
MYL2
PPP1R12A
NAP1L1
NFYB
NOS1
NTS
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
PAWR
CDK17
SLC25A3
PLA2G1B
PMCH
POLE
PPP1CC
PRKAB1
PSMD9
PXMP2
PXN
RAN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
SNRPF
SYT1
TBX5
TBX3
HNF1A
TDG
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UBE2N
UNG
ZNF10
ZNF26
ZNF84
ZNF140
ALX1
CDK2AP1
BRAP
ULK1
EEA1
RASAL1
PPFIA2
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
GALNT4
CRADD
HRK
ADAM1
LIN7A
SOCS2
HCAR3
HIP1R
RASSF9
PIWIL1
CABP1
NCOR2
WSCD2
SART3
KNTC1
MLEC
GIT2
NUAK1
RBM19
RNF10
NR1H4
SH2B3
ARPC3
PLXNC1
MPHOSPH9
CAMKK2
ZNF268
TRAFD1
TMED2
ERP29
CKAP4
GCN1L1
METAP2
SDS
GLIPR1
RAB35
SNRNP35
KERA
KRR1
PRDM4
CIT
PWP1
FICD
NUDT4
FZD10
PHLDA1
MLXIP
RPH3A
P2RX2
FBXO21
SETD1B
UHRF1BP1L
ANKLE2
CUX2
KIAA1033
MED13L
ZDHHC17
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
MGAT4C
FBXW8
HSPB8
HCAR1
UTP20
MRPL42
IFT81
CCDC59
FAM216A
HCFC2
TRHDE
SYCP3
CHST11
GALNT9
CCDC53
CCDC41
GPN3
GLTP
C12orf47
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
SLC6A15
RIC8B
APPL2
SBNO1
DRAM1
SVOP
STAB2
VEZT
GOLGA2P5
ZCCHC8
SCYL2
POLR3B
CHFR
FGD6
WSB2
NDUFA12
DIABLO
ANKS1B
CHPT1
TMCC3
PITPNM2
EP400
DHX37
FBRSL1
DDX55
NTN4
TRPV4
LHX5
SUDS3
ACTR6
C12orf43
VPS33A
RSRC2
AACS
NUP37
DDX54
NOC4L
GNPTAB
B3GNT4
TCTN1
ACSS3
OGFOD2
VPS37B
BBS10
C12orf49
TCTN2
NAA25
SLC24A6
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
KCTD10
USP44
SLC41A2
LRRIQ1
C12orf26
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
CAPS2
UNC119B
USP30
ORAI1
RNFT2
C12orf34
C12orf52
MGC14436
ANKRD13A
NAV3
TMEM116
UBE3B
C12orf23
C12orf29
C12orf65
TMEM132C
CCDC64
SDSL
TMEM132B
OSBPL8
IQCD
LOC116437
DEPDC4
CCDC38
C12orf45
TMEM132D
SLC15A4
NEDD1
SLC9A7P1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
BRI3BP
AMDHD1
GLIPR1L2
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
TSPAN19
E2F7
LOC144481
LOC144486
RAD9B
FAM109A
LOC144742
KRT19P2
TMTC2
TMTC3
C12orf50
ALDH1L2
SLC5A8
PPTC7
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
PLBD2
FAM71C
RMST
C12orf12
SLC17A8
GNN
LRRC43
TCP11L2
LOC255480
LOC256021
GLIPR1L1
POC1B
OTOGL
GPR133
MORN3
LOC283392
GAS2L3
LINC00485
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
DDX51
MMAB
HCAR2
LOC338758
TMEM119
LOC338799
C12orf74
EP400NL
RILPL1
PTPRQ
C12orf42
IL31
C12orf75
CCDC42B
TMEM233
SETD8
LOC387895
MKRN9P
C12orf76
LOC400084
FLJ37505
MIR135A2
C12orf37
PLEKHG7
LOC440117
FLJ31485
NUDT4P1
MIR331
EID3
ATXN7L3B
CLLU1OS
CLLU1
MIR492
MAP1LC3B2
LOC643339
LOC643770
LOC647589
SNORA49
SNORA53
MIR617
MIR618
MIR620
LOC728084
C12orf73
LOC728739
LOC100128191
LOC100128554
LOC100130238
LOC100131138
LOC100131733
LOC100190940
LINC00173
LOC100287944
ZNF605
MIR1252
MIR1827
MIR1178
MIR1251
MIR4303
MIR4304
MIR3685
MIR3612
MIR3652
MIR3922
MIR3908
LOC100505978
LOC100506649
LOC100506668
LOC100507055
LOC100507066
LOC100507091
LOC100507206
LOC100507377
POC1B-GALNT4
ZNF664-FAM101A
MIR4699
MIR4498
MIR548AL
MIR4472-2
MIR4700
MIR4497

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp22.2.

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

Genes
CRLF2
P2RY8
hsa-mir-651
AMELX
SLC25A6
SHROOM2
ARHGAP6
STS
ARSD
ARSE
ARSF
ASMT
CLCN4
CSF2RA
HCCS
IL3RA
KAL1
CD99
MID1
GPR143
PRKX
PRPS2
SHOX
TBL1X
XG
GTPBP6
HDHD1
AKAP17A
PNPLA4
ASMTL
GYG2
ZBED1
FRMPD4
MSL3
MXRA5
VCX
PPP2R3B
VCX2
VCX3A
PLCXD1
WWC3
NLGN4X
ASMTL-AS1
FAM9A
FAM9B
DHRSX
PPP2R3B-AS1
ARSH
LOC389906
CD99P1
VCX3B
MIR651
CXorf28
XGPY2
LOC100288814
LINC00102
MIR3690
MIR4770
MIR4767

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p25.2.

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

Genes
CCND3
DAXX
FANCE
HMGA1
IRF4
PIM1
POU5F1
TRIM27
DEK
TFEB
HIST1H4I
hsa-mir-548u
hsa-mir-133b
hsa-mir-586
hsa-mir-1275
hsa-mir-219-1
hsa-mir-1236
hsa-mir-877
hsa-mir-3143
hsa-mir-548a-1
ABCF1
CRISP1
AGER
AIF1
ATP6V1G2
BAK1
CFB
BMP5
BMP6
DST
BPHL
BTN1A1
BYSL
C2
C4A
C4B
DDR1
RUNX2
CDC5L
CDKN1A
CDSN
CLIC1
CLPS
COL11A2
ATF6B
MAPK14
CSNK2B
CYP21A2
CYP21A1P
DNAH8
DOM3Z
DSP
E2F3
EDN1
SERPINB1
SLC29A1
F13A1
FKBP5
FOXF2
FOXC1
GABBR1
GCNT2
GCLC
GLO1
GLP1R
GMDS
GMPR
GNL1
GPLD1
GPX5
GRM4
GSTA1
GSTA2
GSTA3
GSTA4
GTF2H4
GUCA1A
GUCA1B
HIST1H1C
HIST1H1D
HIST1H1E
HIST1H1B
HIST1H1T
HIST1H2AE
HIST1H2AD
HIST1H2BD
HIST1H2BB
HIST1H1A
HCRTR2
HFE
HIVEP1
HLA-A
HLA-B
HLA-C
HLA-DMA
HLA-DMB
HLA-DOA
HLA-DOB
HLA-DPA1
HLA-DPB1
HLA-DPB2
HLA-DQA1
HLA-DQA2
HLA-DQB1
HLA-DQB2
HLA-DRA
HLA-DRB1
HLA-DRB5
HLA-DRB6
HLA-E
HLA-F
HLA-G
HLA-H
HLA-J
HLA-L
HSPA1A
HSPA1B
HSPA1L
HSP90AB1
ID4
IL17A
ITPR3
JARID2
KIFC1
LTA
LTB
MAK
MCM3
MDFI
MEA1
MEP1A
MICB
MLN
MOCS1
MOG
MSH5
MUT
RPL10A
NEDD9
NEU1
NFKBIE
NFKBIL1
NFYA
NQO2
NOTCH4
PBX2
PEX6
PGC
PGK2
PHF1
SERPINB6
SERPINB9
PKHD1
POLH
PPARD
PPP1R10
PPP2R5D
PRIM2
MAPK13
PRL
PSMB8
PSMB9
PTK7
RGL2
PRPH2
RHAG
RING1
BRD2
RNF5
RPS10
RPS18
RREB1
RXRB
VPS52
ATXN1
SRSF3
SKIV2L
SLC17A1
SNRPC
SOX4
SRF
SRPK1
SSR1
TAF11
TAP1
TAP2
TAPBP
TBCC
TCF19
TCP11
PPP1R11
TEAD3
TFAP2A
TFAP2B
TNF
TNXA
TNXB
TPMT
CRISP2
TUBB2A
TULP1
VARS
VEGFA
ZNF76
ZNF165
TRIM26
ZNF184
ZNF187
ZNF192
ZNF193
ZNF204P
ALDH5A1
PRRC2A
BAG6
GPANK1
DDX39B
ABHD16A
SLC39A7
HSD17B8
OR2H2
RDBP
LST1
PLA2G7
HIST1H2AI
HIST1H2AK
HIST1H2AJ
HIST1H2AL
HIST1H2AC
HIST1H2AB
HIST1H2AM
HIST1H2BG
HIST1H2BL
HIST1H2BN
HIST1H2BM
HIST1H2BF
HIST1H2BE
HIST1H2BH
HIST1H2BI
HIST1H2BC
HIST1H2BO
HIST1H3A
HIST1H3D
HIST1H3C
HIST1H3E
HIST1H3I
HIST1H3G
HIST1H3J
HIST1H3H
HIST1H3B
HIST1H4A
HIST1H4D
HIST1H4F
HIST1H4K
HIST1H4J
HIST1H4C
HIST1H4H
HIST1H4B
HIST1H4E
HIST1H4L
HIST1H4G
CMAHP
DHX16
SUPT3H
GCM1
KCNK5
B3GALT4
RIPK1
SYNGAP1
STK19
IER3
PRPF4B
HIST1H3F
HIST1H2AG
HIST1H2BJ
RNF8
GCM2
WDR46
ZBTB22
CD83
PPT2
CDYL
NCR2
LY86
MED20
SLC25A27
EEF1E1
BAG2
POLR1C
MAD2L1BP
MDC1
TRAM2
FAM65B
ZSCAN12
CUL7
KIAA0319
NUP153
RANBP9
SLC17A4
TRIM10
FLOT1
RCAN2
SLC17A2
HCG9
PRSS16
CRISP3
BTN3A3
BTN2A2
ECI2
PFDN6
HMGN4
TRIM38
CAP2
UBD
AGPAT1
SCGN
C6orf108
C6orf10
FARS2
CNPY3
SLC17A3
RPP40
FRS3
SLC22A7
HCP5
EHMT2
APOBEC2
TRIM31
BTN3A2
BTN3A1
BTN2A1
CAPN11
NUDT3
NRM
STK38
ICK
ENPP4
FTSJD2
CUL9
ANKS1A
UBR2
SIRT5
DAAM2
KIAA0240
DDAH2
CD2AP
MTCH1
ZNF318
SPDEF
YIPF3
USP49
ZNF451
OR2B6
FAM50B
FBXO9
OR12D2
OR11A1
OR2W1
OR2J2
OR2H1
SNORD52
SNORD48
BRPF3
GNMT
TNFRSF21
TINAG
MRPS18B
TMEM14A
C6orf15
MYLIP
ABT1
PRICKLE4
PACSIN1
ZNRD1
DEF6
C6orf48
SLC35B3
GMNN
MRPL2
TBC1D7
NRN1
CYP39A1
NOL7
FAM8A1
DCDC2
ETV7
TMEM14C
TDP2
CUTA
PPIL1
RAB23
CLIC5
TREM2
TREM1
HCG4
GFOD1
HMGCLL1
CCHCR1
GTPBP2
BTN2A3P
UHRF1BP1
ELOVL2
CDKAL1
PAK1IP1
CENPQ
MRPS18A
MRPS10
LRRC1
TMEM63B
LRRC16A
TBC1D22B
EXOC2
SAYSD1
TRERF1
ACOT13
APOM
BTNL2
TRIM39
WRNIP1
DUSP22
LYRM4
VARS2
MRS2
LRFN2
AARS2
XPO5
KIAA1586
CPNE5
LSM2
C6orf47
LY6G5B
LY6G6D
ENPP5
ELOVL5
ZFAND3
SLC22A23
MUTED
CCDC90A
GPSM3
FKBPL
KIF13A
ZNF323
C6orf106
MRPL14
DLK2
LY6G6E
ZNF322
TREML2
RPP21
ATAT1
ZKSCAN3
ZSCAN16
RNF39
SLC44A4
VWA7
C6orf25
LY6G6C
LY6G5C
PRR3
ZNRD1-AS1
PRRT1
EGFL8
HCG4B
TXNDC5
COL21A1
C6orf62
OR5V1
OR2B2
OR12D3
TMEM14B
RIOK1
TFAP2D
KCNK16
DTNBP1
MNF1
PGBD1
TTBK1
ADTRP
HIST1H2AH
HIST1H2BK
PAQR8
RRP36
KCNK17
ABCC10
TRIM15
KLC4
MLIP
TJAP1
POM121L2
FOXQ1
IL17F
EFHC1
BTBD9
SCAND3
FOXP4
KLHDC3
SLC26A8
MAS1L
IP6K3
TAF8
C6orf141
HUS1B
TRIM40
DPCR1
NRSN1
SNRNP48
MBOAT1
HDGFL1
C6orf195
CCDC167
PSORS1C1
PSORS1C2
PPP1R18
PTCRA
TCTE1
TRIM39-RPP21
TUBB
PIP5K1P1
BEND6
GSTA5
OPN5
GPR115
GPR116
TDRD6
SPATS1
C6orf223
RSPH9
LRRC73
TREML2P1
LOC221442
C6orf130
KIF6
TMEM217
FGD2
PI16
C6orf89
ARMC12
C6orf1
LEMD2
ZBTB9
ZBTB12
C6orf136
ZSCAN12P1
HIST1H2AA
KDM1B
RBM24
RNF182
PHACTR1
C6orf228
SYCP2L
LINC00518
PXDC1
MGC39372
FAM83B
GPR111
TSPO2
UNC5CL
KCTD20
PXT1
LHFPL5
SCUBE3
ZSCAN23
NKAPL
TOB2P1
FAM217A
DEFB110
DEFB112
DEFB113
DEFB114
HCG27
RNF144B
HIST1H2BA
GPX6
NCR3
LY6G6F
MDGA1
GPR110
ZNF311
LOC285768
LY86-AS1
CAGE1
LOC285819
HLA-F-AS1
HCG22
LOC285847
PNPLA1
TREML4
RPL7L1
RNF5P1
MYLK4
IFITM4P
CLPSL1
TREML1
TREML3
ZNF391
ZFP57
TUBB2B
SLC35B2
C6orf52
HCG26
KAAG1
GUSBP4
NHLRC1
ZKSCAN4
GUSBP2
VN1R10P
HIST1H2APS1
PSMG4
SFTA2
CLPSL2
C6orf222
GLYATL3
GFRAL
MUC21
DKFZP686I15217
FLJ23152
LINC00340
LOC401242
MCCD1
SAPCD1
LINC00336
FLJ41649
CRIP3
KLHL31
DEFB133
C6orf201
ERVFRD-1
MIR206
MIR219-1
HCG23
HCG25
HCG18
C6orf226
TMEM151B
OR2B3
OR2J3
OR14J1
OR10C1
ATP6V0CP3
PTCHD4
MIR133B
GGNBP1
HCG11
LOC554223
C6orf132
RPS16P5
PPP1R3G
SNORA38
SNORD32B
SNORD84
SNORD117
MIR548A1
MIR586
HULC
LOC729177
LOC730101
GSTA7P
TDRG1
TMEM170B
SCARNA27
MIR877
LOC100129636
LOC100130275
LOC100130357
PSORS1C3
LOC100131047
LOC100131289
LOC100132354
LINC00240
TOMM6
LOC100270746
LOC100287718
LOC100293534
LOC100294145
MIR1275
MIR1236
MIR3143
MIR3925
MIR3691
LOC100506207
LOC100506409
LOC100507173
LOC100507194
LOC100507362
MICA
LOC100507463
LOC100507547
LOC100507584
MUC22
LOC100508120
MUTED-TXNDC5
EEF1E1-MUTED
RPS10-NUDT3
MSH5-SAPCD1
ATP6V1G2-DDX39B
PPT2-EGFL8
MIR4647
MIR4641
MIR4646
MIR4640
MIR4639
MIR4645
MIR4642
MIR4462

Genes in Wide Peak

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

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

Genes
FGFR3
WHSC1
PHOX2B
hsa-mir-574
hsa-mir-1255b-1
hsa-mir-4275
hsa-mir-573
hsa-mir-218-1
hsa-mir-572
hsa-mir-3138
hsa-mir-548i-2
hsa-mir-95
hsa-mir-4274
hsa-mir-943
hsa-mir-571
ADD1
ADRA2C
APBB2
RHOH
ATP5I
NKX3-2
BST1
CCKAR
CD38
CNGA1
CRMP1
CTBP1
DGKQ
DHX15
DRD5
EVC
GABRA2
GABRA4
GABRB1
GABRG1
GAK
GRK4
HTT
HGFAC
UBE2K
HMX1
IDUA
RBPJ
LETM1
LRPAP1
MSX1
MYL5
PCDH7
PDE6B
PPP2R2C
QDPR
RFC1
RGS12
RNF4
RPL9
S100P
SH3BP2
SOD3
TEC
TLR1
TXK
UCHL1
UGDH
WFS1
WHSC2
ZNF141
SLBP
ACOX3
CPZ
NOP14
FAM193A
PROM1
LDB2
SLIT2
RAB28
KIAA0232
WDR1
HS3ST1
FGFBP1
C4orf6
MFSD10
MAEA
TLR6
PCGF3
ATP8A1
SPON2
TACC3
SLC30A9
SLC34A2
MXD4
CORIN
PTTG2
CPLX1
SLC26A1
PPARGC1A
LIAS
LIMCH1
TBC1D1
SEL1L3
PDS5A
MAN2B2
FBXL5
D4S234E
FAM184B
GPR78
ZCCHC4
ANAPC4
LAP3
KLHL5
SEPSECS
KLF3
STX18
FGFRL1
CYTL1
SH3TC1
RBM47
PIGG
DCAF16
OCIAD1
COMMD8
TMEM33
LGI2
PGM2
C4orf19
TBC1D19
PI4K2B
CNO
STK32B
CHRNA9
LYAR
N4BP2
SLC2A9
ATP10D
KIAA1239
TBC1D14
SORCS2
CC2D2A
SLAIN2
STIM2
KIAA1530
WDR19
ZFYVE28
GBA3
AFAP1
GUF1
NCAPG
TNIP2
HAUS3
FLJ13197
NSUN7
ABCA11P
TMEM156
CWH43
GRPEL1
MED28
KCNIP4
TLR10
FGFBP2
MFSD7
TMEM175
ABLIM2
AFAP1-AS1
TMEM128
ZNF518B
CCDC149
C4orf42
TMEM129
FAM114A1
MRFAP1
LOC93622
TADA2B
HTRA3
C1QTNF7
MRFAP1L1
CLNK
ARAP2
OCIAD2
GNPDA2
CPEB2
EVC2
PACRGL
OTOP1
NFXL1
NIPAL1
SHISA3
ZNF595
LOC152742
JAKMIP1
KLB
FAM53A
METTL19
GPR125
ZBTB49
COX7B2
ZNF721
SLC10A4
C4orf34
TAPT1
FLJ39653
LCORL
ZNF718
CCDC96
BOD1L
DCAF4L1
CRIPAK
LOC285484
DOK7
FLJ35424
RNF212
YIPF7
FRYL
LOC285540
LOC285547
LOC285548
FAM200B
C4orf10
ZAR1
NAT8L
LOC344967
C4orf44
FAM86EP
POLN
KCNIP4-IT1
KCTD8
C4orf52
BEND4
GRXCR1
USP17L6P
USP17
HSP90AB2P
C4orf48
DTHD1
LOC401127
LOC402160
MIR218-1
LOC441009
ZNF876P
DEFB131
CLRN2
LOC650293
ZNF732
SCARNA22
MIR572
MIR573
MIR574
LOC728369
LOC728373
LOC728379
USP17L5
LOC728393
LOC728400
LOC728405
FLJ36777
RELL1
PSAPL1
MIR943
LOC100129917
LOC100129931
LOC100130872
LOC100133461
MIR548I2
TMED11P
MIR4274
MIR4275
MIR3138
SLIT2-IT1
LOC100505912
LOC100507266
MIR378D1
MIR548AJ2
MIR4802
MIR4800
MIR4801
MIR4798
HTT-AS1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q22.1.

Table S74. 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
hsa-mir-1261
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

Arm-level results

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

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.25 | -1.01 | 1 | 0.40 | 4.04 | 8.27e-05
1q | 1955 | 0.44 | 4.78 | 4.48e-06 | 0.27 | -0.712 | 1
2p | 924 | 0.46 | 3.06 | 0.00441 | 0.10 | -7.1 | 1
2q | 1556 | 0.32 | -0.231 | 1 | 0.12 | -6.2 | 1
3p | 1062 | 0.27 | -1.59 | 1 | 0.81 | 15.3 | 0
3q | 1139 | 0.69 | 9.63 | 0 | 0.61 | 6.48 | 1.62e-10
4p | 489 | 0.15 | -5.44 | 1 | 0.65 | 8.31 | 0
4q | 1049 | 0.11 | -6.11 | 1 | 0.57 | 7.26 | 9.47e-13
5p | 270 | 0.64 | 5.9 | 3.61e-08 | 0.62 | 5.11 | 5.4e-07
5q | 1427 | 0.15 | -3.66 | 1 | 0.73 | 14 | 0
6p | 1173 | 0.26 | -2.9 | 1 | 0.29 | -2.04 | 1
6q | 839 | 0.21 | -5.14 | 1 | 0.29 | -2.82 | 1
7p | 641 | 0.56 | 5.2 | 6.7e-07 | 0.26 | -3.39 | 1
7q | 1277 | 0.50 | 5.2 | 6.7e-07 | 0.22 | -3.32 | 1
8p | 580 | 0.41 | 0.269 | 1 | 0.72 | 10.3 | 0
8q | 859 | 0.54 | 5.36 | 5.62e-07 | 0.23 | -3.88 | 1
9p | 422 | 0.30 | -2.23 | 1 | 0.72 | 9.9 | 0
9q | 1113 | 0.33 | -0.823 | 1 | 0.58 | 7.11 | 2.52e-12
10p | 409 | 0.21 | -5.33 | 1 | 0.47 | 1.85 | 0.0797
10q | 1268 | 0.11 | -6.46 | 1 | 0.45 | 3.7 | 0.000312
11p | 862 | 0.22 | -4.42 | 1 | 0.40 | 0.863 | 0.37
11q | 1515 | 0.24 | -2.77 | 1 | 0.33 | 0.0843 | 0.811
12p | 575 | 0.49 | 2.92 | 0.00646 | 0.17 | -6.02 | 1
12q | 1447 | 0.33 | -0.127 | 1 | 0.14 | -5.9 | 1
13q | 654 | 0.22 | -3.7 | 1 | 0.67 | 9.18 | 0
14q | 1341 | 0.36 | 0.563 | 0.882 | 0.42 | 2.51 | 0.016
15q | 1355 | 0.28 | -1.78 | 1 | 0.36 | 0.61 | 0.493
16p | 872 | 0.23 | -4.16 | 1 | 0.37 | -0.311 | 1
16q | 702 | 0.25 | -3.91 | 1 | 0.43 | 1.33 | 0.199
17p | 683 | 0.19 | -4.52 | 1 | 0.64 | 8.44 | 0
17q | 1592 | 0.33 | 0.169 | 1 | 0.31 | -0.519 | 1
18p | 143 | 0.38 | -1.53 | 1 | 0.40 | -1.04 | 1
18q | 446 | 0.34 | -1.89 | 1 | 0.45 | 1.31 | 0.199
19p | 995 | 0.31 | -1.69 | 1 | 0.43 | 1.83 | 0.0797
19q | 1709 | 0.40 | 2.64 | 0.014 | 0.34 | 0.874 | 0.37
20p | 355 | 0.56 | 4.78 | 4.48e-06 | 0.23 | -4.46 | 1
20q | 753 | 0.52 | 4.43 | 2.14e-05 | 0.22 | -4.33 | 1
21q | 509 | 0.23 | -4.05 | 1 | 0.60 | 6.52 | 1.41e-10
22q | 921 | 0.54 | 5.2 | 6.7e-07 | 0.35 | -0.692 | 1
Xq | 1312 | 0.17 | -5.22 | 1 | 0.30 | -1.4 | 1

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/LUSC/1669156/2.GDAC_MergeDataFiles.Finished/LUSC.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 289 Input Tumor Samples.

Tumor Sample Names
TCGA-18-3406-01A-01D-0978-01
TCGA-18-3407-01A-01D-1969-01
TCGA-18-3408-01A-01D-0978-01
TCGA-18-3409-01A-01D-0978-01
TCGA-18-3410-01A-01D-1969-01
TCGA-18-3411-01A-01D-1969-01
TCGA-18-3412-01A-01D-0978-01
TCGA-18-3414-01A-01D-0978-01
TCGA-18-3415-01A-01D-0978-01
TCGA-18-3416-01A-01D-0978-01

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
Copyright © 2012 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle