Head and Neck 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 288 tumor samples used in this analysis: 27 significant arm-level results, 28 significant focal amplifications, and 41 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 - 28 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
--- | --- | --- | --- | ---
11q13.3 | 3.2293e-154 | 3.2293e-154 | chr11:70036108-70236792 | 4
3q26.33 | 3.6226e-31 | 3.6226e-31 | chr3:177462042-183101851 | 25
7p11.2 | 2.9605e-25 | 2.9605e-25 | chr7:55040275-55429016 | 1
8p11.23 | 4.26e-14 | 5.0161e-14 | chr8:38147031-38270604 | 3
8q24.21 | 2.6447e-10 | 2.9036e-09 | chr8:128153806-128467060 | 2
9p13.3 | 3.037e-10 | 5.9723e-09 | chr9:35438295-36015652 | 27
13q22.1 | 9.8483e-08 | 9.8483e-08 | chr13:73865469-74043687 | 0 [KLF5]
12q15 | 5.5733e-07 | 5.5733e-07 | chr12:69215691-70378943 | 14
2q31.2 | 8.6304e-08 | 1.121e-06 | chr2:178072000-178247860 | 6
7q22.1 | 1.238e-05 | 1.238e-05 | chr7:98225037-100656111 | 84
20q11.22 | 3.5596e-05 | 3.5596e-05 | chr20:31799297-32632528 | 14
18q11.2 | 4.8059e-05 | 4.8059e-05 | chr18:20718726-20946198 | 2
9p23 | 6.8319e-07 | 9.4125e-05 | chr9:13397807-14321078 | 3
2q11.2 | 2.5751e-05 | 0.00019723 | chr2:97503963-97572142 | 4
17q12 | 0.0026961 | 0.0026961 | chr17:37658857-38028984 | 13
18p11.31 | 0.0040129 | 0.0040129 | chr18:2830250-4802485 | 11
11p13 | 0.00057542 | 0.0081034 | chr11:35861175-35879772 | 0 [TRIM44]
5p15.33 | 0.00061654 | 0.010522 | chr5:1-1415403 | 26
12p13.33 | 0.015286 | 0.015286 | chr12:1-6057976 | 52
6p12.1 | 0.015743 | 0.022234 | chr6:53071691-55852153 | 12
6q12 | 0.027086 | 0.036952 | chr6:64257063-64568802 | 3
8q11.21 | 0.001359 | 0.038276 | chr8:49118224-50070119 | 3
5p12 | 0.016665 | 0.088725 | chr5:39932337-50133343 | 35
1q21.2 | 0.14088 | 0.14088 | chr1:120523956-149884926 | 84
14q11.2 | 0.16425 | 0.16425 | chr14:21146585-21711097 | 22
11p11.2 | 0.0075644 | 0.21683 | chr11:44546506-46821077 | 31
15q26.3 | 0.23859 | 0.23859 | chr15:90053056-102531392 | 87
Xq28 | 0.24274 | 0.24274 | chrX:151321444-155270560 | 110

Genes in Wide Peak

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

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

Genes
hsa-mir-548k
PPFIA1
FADD
MIR548K

Genes in Wide Peak

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

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

Genes
PIK3CA
SOX2
ACTL6A
NDUFB5
FXR1
USP13
KCNMB2
MCF2L2
ATP11B
LAMP3
KCNMB3
ZNF639
PEX5L
DCUN1D1
MFN1
MCCC1
MRPL47
GNB4
ZMAT3
B3GNT5
DNAJC19
TTC14
CCDC39
SOX2-OT
FLJ46066

Genes in Wide Peak

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

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

Genes
EGFR

Genes in Wide Peak

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

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

Genes
FGFR1
WHSC1L1
LETM2

Genes in Wide Peak

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

Table S5. 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 9p13.3.

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

Genes
CA9
CD72
NPR2
RMRP
TESK1
TLN1
TPM2
RGP1
RUSC2
CREB3
SPAG8
SIT1
TMEM8B
OR2S2
GBA2
HINT2
C9orf100
FP588
LOC158376
ATP8B5P
CCDC107
C9orf128
OR13J1
HRCT1
MSMP
FAM166B
MIR4667

Genes in Wide Peak

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

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

Genes
MDM2
hsa-mir-1279
CPM
LYZ
YEATS4
CCT2
FRS2
CPSF6
RAB3IP
BEST3
LRRC10
MIR1279
MIR3913-2
MIR3913-1

Genes in Wide Peak

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

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

Genes
NFE2L2
hsa-mir-3128
HNRNPA3
LOC100130691
MIR3128
MIR4444-1

Genes in Wide Peak

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

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

Genes
hsa-mir-106b
ACHE
AZGP1
CYP3A7
CYP3A4
CYP3A5
EPHB4
EPO
GNB2
AGFG2
LRCH4
MCM7
NPTX2
PCOLCE
PMS2P1
TAF6
TFR2
TRIP6
ZAN
ZNF3
ZKSCAN1
ZSCAN21
TRRAP
BUD31
AP4M1
ATP5J2
MUC12
ARPC1B
POP7
ARPC1A
STAG3
CPSF4
COPS6
PDAP1
ZKSCAN5
PTCD1
FBXO24
PILRB
PILRA
ACTL6B
SRRT
ZCWPW1
C7orf43
MEPCE
SLC12A9
SMURF1
MOSPD3
GIGYF1
CYP3A43
ZNF655
PVRIG
GAL3ST4
OR2AE1
TSC22D4
ZNF394
MYH16
TRIM4
ZNF498
FAM200A
PPP1R35
GPC2
TMEM130
NYAP1
CNPY4
MBLAC1
ZNF789
GJC3
GATS
C7orf59
KPNA7
C7orf61
UFSP1
MIR106B
MIR25
MIR93
SPDYE3
AZGP1P1
LOC100129845
LOC100289187
SAP25
MIR3609
ATP5J2-PTCD1
MIR4658
CYP3A7-CYP3AP1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q11.22.

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

Genes
E2F1
SNTA1
CBFA2T2
PXMP4
RALY
BPIFA1
CDK5RAP1
NECAB3
ZNF341
BPIFB1
BPIFA3
C20orf144
CHMP4B
ACTL10

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
TMEM241
CABLES1

Genes in Wide Peak

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

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

Genes
NFIB
FLJ41200
C9orf146

Genes in Wide Peak

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

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

Genes
ANKRD39
FAM178B
SEMA4C
ANKRD23

Genes in Wide Peak

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

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

Genes
ERBB2
GRB7
NEUROD2
PNMT
TCAP
STARD3
IKZF3
CDK12
PPP1R1B
MIEN1
PGAP3
ZPBP2
MIR4728

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 18p11.31.

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

Genes
TGIF1
MYOM1
DLGAP1
LPIN2
MYL12A
EMILIN2
MYL12B
LOC201477
LOC284215
FLJ35776
LOC727896

Genes in Wide Peak

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

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

Genes
SDHA
SLC6A3
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
PP7080
CEP72
AHRR
BRD9
ZDHHC11
CLPTM1L
NKD2
C5orf55
CCDC127
PLEKHG4B
SLC6A19
SLC6A18
LRRC14B
LOC100506688
MIR4457
MIR4456
MIR4635

Genes in Wide Peak

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

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

Genes
CCND2
KDM5A
CACNA1C
FGF6
FKBP4
FOXM1
KCNA1
KCNA5
KCNA6
NDUFA9
NINJ2
NTF3
RAD52
SLC6A12
SLC6A13
TEAD4
TULP3
FGF23
DYRK4
AKAP3
RAD51AP1
TSPAN9
ERC1
GALNT8
ITFG2
PRMT8
PARP11
ANO2
C12orf4
C12orf5
WNK1
ADIPOR2
WNT5B
C12orf32
NRIP2
CCDC77
EFCAB4B
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 6p12.1.

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

Genes
BMP5
GCLC
HCRTR2
TINAG
HMGCLL1
LRRC1
ELOVL5
MLIP
FAM83B
GFRAL
KLHL31
RPS16P5

Genes in Wide Peak

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

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

Genes
PTP4A1
PHF3
EYS

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8q11.21.

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

Genes
SNAI2
EFCAB1
C8orf22

Genes in Wide Peak

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

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

Genes
hsa-mir-1274a
C6
C7
FGF10
GHR
HMGCS1
OXCT1
PRKAA1
PTGER4
RPL37
SEPP1
ZNF131
PAIP1
MRPS30
NNT
TTC33
FBXO4
CCL28
C5orf28
PARP8
CARD6
EMB
HEATR7B2
LOC153684
NIM1
C5orf51
PLCXD3
HCN1
C5orf34
C5orf39
SNORD72
LOC648987
CCDC152
LOC100132356
LOC100506548

Genes in Wide Peak

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

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

Genes
BCL9
NOTCH2
PDE4DIP
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
FCGR1A
FCGR1B
FMO5
GJA5
GJA8
PDZK1
PRKAB2
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
ITGA10
PEX11B
SEC22B
CHD1L
SV2A
RBM8A
PIAS3
POLR3C
TXNIP
CD160
NBPF14
RNF115
BOLA1
ACP6
GPR89B
FAM91A2
POLR3GL
GNRHR2
HIST2H3C
LIX1L
HFE2
ANKRD35
PPIAL4A
PDIA3P
NBPF11
NUDT17
NBPF15
ANKRD34A
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
LOC375010
NOTCH2NL
FLJ39739
LOC388692
NBPF9
HIST2H2BF
HIST2H4B
PPIAL4G
PPIAL4D
LOC645166
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
LOC100130000
NBPF10
FCGR1C
LOC100286793
LOC100289211

Genes in Wide Peak

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

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

Genes
ANG
HNRNPC
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
EDDM3A
SLC39A2
ZNF219
ARHGEF40
NDRG2
EDDM3B
METTL17
RNASE7
TPPP2
RNASE8
LOC283624
OR5AU1
RNASE13
ECRP
C14orf176

Genes in Wide Peak

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

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

Genes
CREB3L1
hsa-mir-3160-2
ARHGAP1
CHRM4
CRY2
F2
CD82
MDK
DGKZ
CHST1
PEX16
MAPK8IP1
TP53I11
ATG13
CKAP5
PHF21A
SLC35C1
AMBRA1
PRDM11
SYT13
ZNF408
TSPAN18
GYLTL1B
C11orf94
LOC221122
HARBI1
DKFZp779M0652
SNORD67
MIR3160-2
MIR3160-1
MIR4688

Genes in Wide Peak

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

Table S25. 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
ALDH1A3
ANPEP
CHD2
FES
IGF1R
MAN2A2
MEF2A
FURIN
PCSK6
PLIN1
SNRPA1
NR2F2
ST8SIA2
PEX11A
IQGAP1
PRC1
SV2B
AP3S2
SEMA4B
CIB1
CHSY1
SYNM
GABARAPL3
VPS33B
OR4F4
SLCO3A1
NGRN
LINS
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
LOC283761
FAM169B
ZNF774
C15orf38
KIF7
ZNF710
HDDC3
WASH3P
FLJ42289
C15orf58
OR4F6
OR4F15
FAM174B
LOC400456
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 Xq28.

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

Genes
MTCP1
hsa-mir-1184-3
hsa-mir-1184-2
hsa-mir-1184-1
hsa-mir-718
hsa-mir-105-2
ABCD1
ARHGAP4
ATP2B3
ATP6AP1
AVPR2
BGN
CETN2
CLIC2
CTAG1B
TEX28
DKC1
DNASE1L1
DUSP9
EMD
F8
FLNA
G6PD
GABRA3
OPN1MW
GDI1
HCFC1
IDH3G
IL9R
IRAK1
L1CAM
MAGEA1
MAGEA2
MAGEA3
MAGEA6
MAGEA12
MECP2
MPP1
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SSR4
VAMP7
TAZ
VBP1
ZNF185
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
IKBKG
FAM50A
BCAP31
SPRY3
ZNF275
TREX2
SRPK3
SNORA70
PNMA3
CTAG2
NSDHL
TMLHE
PLXNA3
HAUS7
GABRQ
PDZD4
FAM3A
FUNDC2
BRCC3
H2AFB3
PNMA6A
FAM58A
PNMA5
RAB39B
GAB3
PNCK
ZFP92
CSAG1
CTAG1A
MAGEA2B
LINC00204B
CSAG3
MIR105-1
MIR105-2
H2AFB2
H2AFB1
F8A2
F8A3
SNORA36A
SNORA56
OPN1MW2
CSAG2
MIR767
CXorf68
LINC00204A
MTCP1NB
PNMA6C
PNMA6D
MIR1184-1
MIR718
MIR3202-2
MIR1184-3
MIR1184-2
MIR3202-1
LOC100507404

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 - 41 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 | 1.3734e-117 | 2.3909e-106 | chr9:21865498-21997722 | 2
8p23.2 | 4.3521e-47 | 4.3521e-47 | chr8:2079140-6262191 | 1
4q35.2 | 1.0621e-18 | 4.4182e-18 | chr4:187475875-188227950 | 1
11q23.1 | 1.6583e-17 | 1.6583e-17 | chr11:108811192-116715687 | 66
2q22.1 | 2.4033e-23 | 1.0394e-15 | chr2:139655617-143637838 | 1
7q36.1 | 2.4876e-13 | 2.5979e-13 | chr7:148117946-153767963 | 72
18q23 | 9.7157e-15 | 2.4796e-12 | chr18:67995567-78077248 | 36
13q12.11 | 4.8115e-13 | 3.4577e-11 | chr13:19690077-23755126 | 25
1p13.2 | 7.2591e-11 | 3.3263e-10 | chr1:112530734-149881397 | 156
19p13.3 | 9.4793e-10 | 9.8455e-10 | chr19:1-2790142 | 108
2q37.3 | 9.3123e-15 | 3.0241e-08 | chr2:207173502-243199373 | 325
10p11.21 | 1.7708e-07 | 1.8772e-07 | chr10:34059131-35328087 | 1
5q11.2 | 2.0536e-07 | 3.173e-07 | chr5:58145167-59787985 | 3
9p24.1 | 5.6221e-19 | 1.1651e-06 | chr9:8310705-12693402 | 1
16q23.3 | 2.6159e-06 | 2.6353e-06 | chr16:82159666-83844787 | 4
Xq21.33 | 6.4128e-06 | 6.1775e-06 | chrX:96134519-98718611 | 1
Xp21.3 | 2.2852e-06 | 4.2662e-05 | chrX:27994560-30234516 | 2
2q21.2 | 1.3041e-14 | 4.6298e-05 | chr2:133423352-134889663 | 2
1p36.13 | 1.3277e-05 | 8.4962e-05 | chr1:7829287-20211791 | 174
6p25.3 | 0.00014316 | 0.00014028 | chr6:1101324-2250882 | 4
10q23.31 | 0.0011034 | 0.0011117 | chr10:89617158-90034038 | 2
17q25.3 | 0.0013353 | 0.0012992 | chr17:80698053-80902410 | 2
3p12.2 | 0.00014062 | 0.002505 | chr3:75363575-86988125 | 14
14q11.2 | 0.0023506 | 0.0051864 | chr14:1-31030869 | 166
5q35.2 | 0.0036002 | 0.0053215 | chr5:176521457-176731866 | 2
Xp11.3 | 0.00020539 | 0.0053215 | chrX:44702452-45008304 | 2
13q21.33 | 8.1553e-05 | 0.0077327 | chr13:33071296-73335020 | 168
9q34.3 | 0.01391 | 0.013782 | chr9:139376600-139456211 | 4
3p14.2 | 8.4962e-05 | 0.022318 | chr3:61234833-62281357 | 2
4p15.31 | 0.022879 | 0.022318 | chr4:1-30734965 | 203
4q22.1 | 0.005065 | 0.027255 | chr4:90844993-93240505 | 1
14q32.32 | 0.0086626 | 0.031607 | chr14:81679070-107349540 | 285
3p24.1 | 0.0024643 | 0.060394 | chr3:28799677-30767809 | 2
11p15.4 | 0.083686 | 0.084012 | chr11:1-30035954 | 375
19q13.43 | 0.085069 | 0.084012 | chr19:57166834-59128983 | 76
18q21.2 | 9.8965e-08 | 0.096495 | chr18:48255169-49870310 | 6
16q12.1 | 0.11083 | 0.11166 | chr16:31772318-56969379 | 96
15q15.1 | 0.11939 | 0.11848 | chr15:1-83198330 | 693
9p13.1 | 0.0009189 | 0.19625 | chr9:37902544-71152237 | 54
6q12 | 0.20704 | 0.21559 | chr6:64293011-116264311 | 196
12q24.33 | 0.24546 | 0.24171 | chr12:71029284-133851895 | 455

Genes in Wide Peak

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

Table S27. 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 S28. 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 4q35.2.

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

Genes
FAT1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q23.1.

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

Genes
POU2AF1
SDHD
hsa-mir-4301
hsa-mir-34c
APOA1
APOA4
APOC3
CRYAB
DLAT
DRD2
FDX1
HSPB2
HTR3A
IL18
NCAM1
NNMT
PPP2R1B
PTS
RDX
ZBTB16
ZNF259
HTR3B
ZW10
RBM7
SIK2
CADM1
REXO2
TIMM8B
C11orf71
BTG4
FAM55D
TTC12
C11orf57
TEX12
ARHGAP20
USP28
C11orf1
ALG9
TMPRSS5
BCO2
BUD13
DIXDC1
ZC3H12C
FDXACB1
C11orf52
APOA5
C11orf93
PIH1D2
FAM55A
FAM55B
LAYN
ANKK1
LOC283143
C11orf53
C11orf34
C11orf87
C11orf92
C11orf88
MIR34B
MIR34C
CLDN25
LOC100132078
LOC100288346
MIR4301
HSPB2-C11orf52
MIR4491

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 7q36.1.

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

Genes
EZH2
MLL3
hsa-mir-671
hsa-mir-1975
ABP1
CDK5
GBX1
KCNH2
NOS3
RARRES2
RHEB
SLC4A2
SMARCD3
XRCC2
ZNF212
ZNF282
CUL1
ACCN3
PDIA4
ABCF2
FASTK
ABCB8
SSPO
GIMAP2
ZNF777
TMEM176B
REPIN1
PRKAG2
NUB1
CHPF2
GIMAP4
GIMAP5
TMEM176A
ACTR3B
ZNF398
GALNT11
LRRC61
ZNF767
TMUB1
KRBA1
C7orf29
AGAP3
ZNF786
ASB10
GIMAP8
CRYGN
ZNF425
LOC155060
ZNF746
ATP6V0E2
GALNTL5
GIMAP7
ZNF467
GIMAP1
C7orf33
FABP5P3
ZNF775
LOC285972
ATG9B
WDR86
LOC401431
GIMAP6
ZNF862
ACTR3C
LOC728743
MIR671
LOC100128822
LOC100131176
ZNF783
MIR3907
LOC100505483
GIMAP1-GIMAP5

Genes in Wide Peak

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

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

Genes
CYB5A
GALR1
MBP
NFATC1
ZNF236
CTDP1
ZNF516
TSHZ1
TXNL4A
ADNP2
KCNG2
SALL3
TIMM21
ZNF407
CNDP2
RBFA
PQLC1
NETO1
PARD6G
CNDP1
FAM69C
CBLN2
FBXO15
ZADH2
C18orf62
LOC284276
LOC339298
ATP9B
LOC400655
LOC400657
HSBP1L1
C18orf63
LOC100130522
LOC100131655
LOC100505776
LOC100505817

Genes in Wide Peak

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

Table S34. 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
BASP1P1
ANKRD26P3
LINC00421
MIR4499

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p13.2.

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

Genes
BCL9
NOTCH2
NRAS
PDE4DIP
TRIM33
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
AMPD1
RHOC
ATP1A1
CAPZA1
CASQ2
CD2
CD58
FCGR1A
FCGR1B
FMO5
GJA5
GJA8
HMGCS2
HSD3B1
HSD3B2
IGSF3
MOV10
NGF
NHLH2
PDZK1
PRKAB2
PTGFRN
SLC16A1
SYCP1
TBX15
TSHB
WNT2B
CSDE1
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
TTF2
ITGA10
PEX11B
CD101
SEC22B
CHD1L
LRIG2
RBM8A
TSPAN2
BCAS2
WARS2
PIAS3
POLR3C
TXNIP
AP4B1
PHTF1
WDR3
MAN1A2
ADAM30
CD160
NBPF14
PTPN22
PHGDH
RNF115
BOLA1
HAO2
ACP6
GPR89B
RSBN1
GDAP2
FAM46C
ST7L
SLC22A15
CTTNBP2NL
OLFML3
FAM91A2
DCLRE1B
VTCN1
SIKE1
TRIM45
VANGL1
REG4
POLR3GL
ATP1A1OS
ZNF697
GNRHR2
MAB21L3
HIST2H3C
LIX1L
HSD3BP4
SYT6
HFE2
ANKRD35
DENND2C
PPIAL4A
PDIA3P
NBPF11
NUDT17
SPAG17
HIPK1
AKR7A2P1
MAGI3
FAM19A3
NBPF15
ANKRD34A
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BC
HIST2H2BA
NBPF7
LOC375010
NOTCH2NL
FLJ39739
LOC388692
NBPF9
BCL2L15
HIST2H2BF
HIST2H4B
LOC643441
LOC644242
PPIAL4G
PPIAL4D
LOC645166
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
MIR942
LOC100130000
NBPF10
FCGR1C
LOC100286793
LOC100287722
LOC100289211
MIR320B1
MIR4256

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
TCF3
FSTL3
hsa-mir-4321
hsa-mir-1909
hsa-mir-3187
hsa-mir-1302-11
AMH
ATP5D
AZU1
HCN2
BSG
CDC34
CIRBP
CNN2
CSNK1G2
CFD
ARID3A
EFNA2
ELANE
GAMT
GNG7
MKNK2
GPX4
GZMM
GADD45B
OAZ1
PALM
POLR2E
POLRMT
PRTN3
PTBP1
RPS15
SGTA
MADCAM1
SF3A2
PPAP2C
AP3D1
MED16
APC2
ABCA7
UQCR11
SBNO2
HMHA1
SHC2
TIMM13
DAZAP1
FGF22
SLC39A3
THEG
LSM7
MBD3
MIER2
PCSK4
C19orf24
PLEKHJ1
BTBD2
RNF126
SPPL2B
WDR18
REXO1
LPPR3
OR4F17
FAM108A1
KLF16
DOT1L
KISS1R
LMNB2
MUM1
MIDN
R3HDM4
C19orf6
TPGS1
REEP6
IZUMO4
SCAMP4
ADAT3
GRIN3B
JSRP1
MOB3A
C19orf21
PLK5
C2CD4C
CIRBP-AS1
C19orf25
ATP8B3
DIRAS1
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 2q37.3.

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

Genes
ATIC
CREB1
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
hsa-mir-1302-4
hsa-mir-2355
hsa-mir-3130-4
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
FZD5
SCG2
CUL3
DGKD
STK16
KLF7
ADAM23
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
LANCL1
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
FASTKD2
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
CPO
MDH1B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
PKI55
C2orf67
LOC151171
LOC151174
METTL21A
CCNYL1
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
PIKFYVE
LOC200726
TIGD1
LOC200772
CCDC108
C2orf72
CXXC11
UNC80
RUFY4
DUSP28
ESPNL
ECEL1P2
LOC348761
C2orf62
RBM44
AQP12A
KLHL30
PLEKHM3
C2orf80
RESP18
C2orf82
OR6B2
DYTN
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
MIR3130-1
MIR3130-2
MIR2355
MIR3132
MIR4269
LOC100507443
UBE2F-SCLY
MIR4439
MIR4776-1
MIR4777
MIR2467
MIR4775
MIR4440
MIR4786
MIR4776-2
MIR4441

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p11.21.

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

Genes
PARD3

Genes in Wide Peak

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

Table S39. 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 9p24.1.

Table S40. 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 16q23.3.

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

Genes
hsa-mir-3182
CDH13
MPHOSPH6
MIR3182

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xq21.33.

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

Genes
RPA4

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp21.3.

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

Genes
IL1RAPL1
DCAF8L1

Genes in Wide Peak

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

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

Genes
NCKAP5
MIR3679

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.13.

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

Genes
PAX7
SDHB
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
RERE
CA6
CAPZB
CASP9
TNFRSF8
CLCN6
CLCNKA
CLCNKB
CORT
DFFA
EPHA2
ENO1
MTOR
HTR6
TNFRSF9
MFAP2
MTHFR
NBL1
NPPA
NPPB
PEX14
PGD
PIK3CD
PLOD1
EXOSC10
RSC1A1
SLC2A5
SRM
TNFRSF1B
ZBTB17
PRDM2
AKR7A2
ALDH4A1
PER3
DHRS3
VAMP3
H6PD
CROCC
MFN2
ANGPTL7
UBE4B
MAD2L2
PDPN
MASP2
UTS2
MST1P2
MST1P9
PADI2
PARK7
CTRC
CLSTN1
AKR7A3
SPEN
KIAA0090
KIF1B
PLEKHM2
KAZN
DNAJC16
UBR4
ATP13A2
TARDBP
PADI4
C1orf144
FBXO2
FBXO6
HSPB7
UBIAD1
PADI1
SLC45A1
CELA2B
MRTO4
PADI3
ERRFI1
FBXO42
RNF186
FBLIM1
PQLC2
CASZ1
TMEM51
ARHGEF10L
VPS13D
NBPF1
NECAP2
RCC2
CTNNBIP1
AGTRAP
PTCHD2
MIIP
CELA2A
NMNAT1
PRAMEF1
PRAMEF2
EFHD2
RSG1
AGMAT
GPR157
SPSB1
TAS1R2
ACTL8
SLC25A33
DDI2
LZIC
CROCCP2
IGSF21
KIAA2013
C1orf158
FBXO44
CROCCP3
FHAD1
RBP7
LRRC38
AADACL3
IFFO2
KLHDC7A
ARHGEF19
C1orf127
C1orf64
SLC2A7
TMEM201
C1orf126
AKR7L
TMCO4
SLC25A34
ESPNP
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
C1orf187
SPATA21
APITD1
TMEM82
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PRAMEF4
PRAMEF13
PRAMEF3
MIR34A
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
PRAMEF7
C1orf200
PRAMEF19
PRAMEF20
LOC649330
PRAMEF22
PRAMEF15
PRAMEF16
SNORA59B
SNORA59A
PRAMEF14
FLJ37453
NPPA-AS1
MIR3675
ENO1-AS1
LOC100506730
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4632

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6p25.3.

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

Genes
FOXF2
FOXC1
GMDS
FOXQ1

Genes in Wide Peak

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

Table S47. 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 17q25.3.

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

Genes
TBCD
ZNF750

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p12.2.

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

Genes
hsa-mir-4273
hsa-mir-1324
GBE1
ROBO1
ROBO2
CADM2
LOC401074
LOC440970
FLJ20518
FAM86DP
ZNF717
FRG2C
MIR1324
MIR4273

Genes in Wide Peak

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

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

Genes
CCNB1IP1
hsa-mir-3171
hsa-mir-4307
hsa-mir-208b
hsa-mir-1201
ANG
APEX1
BCL2L2
CEBPE
CMA1
LTB4R
CTSG
DAD1
FOXG1
GZMH
GZMB
HNRNPC
MMP14
MYH6
MYH7
NEDD8
NFATC4
NOVA1
PNP
NRL
OXA1L
PCK2
PRKD1
PSMB5
PSME1
PSME2
RABGGTA
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
SALL2
TEP1
TGM1
PABPN1
AP1G2
SLC7A7
CPNE6
TOX4
REC8
PARP2
DHRS2
EFS
IRF9
PRMT5
TM9SF1
EDDM3A
DHRS4
RIPK3
SUPT16H
ACIN1
KHNYN
SLC7A8
NGDN
LRP10
TINF2
OR10G3
OR10G2
OR4E2
CIDEB
CHMP4A
STXBP6
SLC39A2
FAM158A
ZNF219
GMPR2
SLC22A17
HAUS4
C14orf119
RNF31
RBM23
C14orf167
OSGEP
ARHGEF40
METTL3
LTB4R2
SDR39U1
RPGRIP1
NDRG2
NYNRIN
HOMEZ
CHD8
C14orf93
ABHD4
EDDM3B
CDH24
METTL17
IL25
THTPA
OR4K5
OR11H2
OR4K1
IPO4
DCAF11
OR4K15
JPH4
RNASE7
RAB2B
AJUBA
ZFHX2
RPPH1
LRRC16B
PPP1R3E
TMEM55B
TTC5
DHRS1
CMTM5
RNASE11
TPPP2
RNASE8
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
KLHL33
MDP1
FITM1
REM2
C14orf21
ADCY4
LOC283624
TSSK4
DHRS4L2
SNORD8
RNASE10
OR6S1
C14orf23
OR4N2
OR4K2
OR4K13
OR4K17
OR4N5
OR11G2
OR11H4
RNASE9
OR5AU1
POTEG
MIR208A
C14orf165
OR11H12
RNASE13
OR4Q3
OR4M1
RNASE12
POTEM
LOC642426
ECRP
C14orf176
CBLN3
SNORD9
DHRS4L1
SNORD126
MIR208B
MIR4307
LOC100505967
NEDD8-MDP1
BCL2L2-PABPN1
MIR548AI
MIR4707

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q35.2.

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

Genes
NSD1
RAB24

Genes in Wide Peak

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

Table S52. 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 13q21.33.

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

Genes
LCP1
RB1
LHFP
TTL
hsa-mir-3169
hsa-mir-1297
hsa-mir-759
hsa-mir-15a
hsa-mir-3168
hsa-mir-621
hsa-mir-4305
ATP7B
RCBTB2
CPB2
DACH1
ELF1
ESD
FOXO1
MLNR
GTF2F2
GUCY1B2
HTR2A
KPNA3
MAB21L1
SMAD9
NEK3
PCDH8
PCDH9
RFC3
RFXAP
ATXN8OS
TPT1
TRPC4
TNFSF11
SUCLA2
DLEU2
TSC22D1
CCNA1
DCLK1
KL
ITM2B
MTRF1
UTP14C
LPAR6
SLC25A15
TRIM13
MRPS31
DLEU1
N4BP2L2
OLFM4
POSTN
SUGT1
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
PDS5B
KIAA0564
ZC3H13
SPG20
LRCH1
INTS6
CKAP2
NUFIP1
NBEA
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
PHF11
UFM1
SOHLH2
ENOX1
RCBTB1
NUDT15
KIAA1704
FAM48A
THSD1
CYSLTR2
SPRYD7
COG6
KLHL1
PCDH20
NAA16
RNASEH2B
DHRS12
BORA
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KBTBD7
EBPL
KBTBD6
STARD13
EPSTI1
ARL11
WDFY2
CG030
LINC00284
CSNK1A1L
PRR20A
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
DGKH
CCDC122
STOML3
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
SLC25A30
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
LINC00550
FREM2
NEK5
THSD1P1
KCTD4
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
MIR15A
MIR16-1
ALG11
MZT1
TSC22D1-AS1
SERPINE3
SNORA31
MIR621
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
TPT1-AS1
MIR1297
MIR548F5
MIR759
MIR320D1
MIR4305
MIR3169
MIR3613
OR7E37P
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
MIR4703
LOC100616668

Genes in Wide Peak

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

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

Genes
NOTCH1
C9orf163
MIR4673
MIR4674

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p14.2.

Table S55. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
PTPRG
ID2B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4p15.31.

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

Genes
FGFR3
WHSC1
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
ATP5I
NKX3-2
BST1
CCKAR
CD38
CRMP1
CTBP1
DGKQ
DHX15
DRD5
EVC
GAK
GRK4
HTT
HGFAC
HMX1
IDUA
RBPJ
LETM1
LRPAP1
MSX1
MYL5
PCDH7
PDE6B
PPP2R2C
QDPR
RGS12
RNF4
S100P
SH3BP2
SOD3
WFS1
WHSC2
ZNF141
SLBP
ACOX3
CPZ
NOP14
FAM193A
PROM1
LDB2
SLIT2
RAB28
KIAA0232
WDR1
HS3ST1
FGFBP1
C4orf6
MFSD10
MAEA
PCGF3
SPON2
TACC3
SLC34A2
MXD4
CPLX1
SLC26A1
PPARGC1A
SEL1L3
MAN2B2
FBXL5
D4S234E
FAM184B
GPR78
ZCCHC4
ANAPC4
LAP3
SEPSECS
STX18
FGFRL1
CYTL1
SH3TC1
PIGG
DCAF16
LGI2
TBC1D19
PI4K2B
CNO
STK32B
LYAR
SLC2A9
TBC1D14
SORCS2
CC2D2A
STIM2
KIAA1530
ZFYVE28
GBA3
AFAP1
NCAPG
TNIP2
HAUS3
ABCA11P
GRPEL1
MED28
KCNIP4
FGFBP2
MFSD7
TMEM175
ABLIM2
AFAP1-AS1
TMEM128
ZNF518B
CCDC149
C4orf42
TMEM129
MRFAP1
LOC93622
TADA2B
HTRA3
C1QTNF7
MRFAP1L1
CLNK
CPEB2
EVC2
PACRGL
OTOP1
ZNF595
LOC152742
JAKMIP1
FAM53A
METTL19
GPR125
ZBTB49
ZNF721
TAPT1
FLJ39653
LCORL
ZNF718
CCDC96
BOD1L
CRIPAK
LOC285484
DOK7
FLJ35424
RNF212
LOC285540
LOC285547
LOC285548
FAM200B
C4orf10
NAT8L
C4orf44
FAM86EP
POLN
KCNIP4-IT1
C4orf52
USP17L6P
USP17
HSP90AB2P
C4orf48
LOC402160
MIR218-1
LOC441009
ZNF876P
DEFB131
CLRN2
LOC650293
ZNF732
SCARNA22
MIR572
MIR573
LOC728369
LOC728373
LOC728379
USP17L5
LOC728393
LOC728400
LOC728405
FLJ36777
PSAPL1
MIR943
LOC100129917
LOC100129931
LOC100130872
LOC100133461
MIR548I2
TMED11P
MIR4274
MIR4275
MIR3138
SLIT2-IT1
LOC100505912
LOC100507266
MIR378D1
MIR548AJ2
MIR4800
MIR4798
HTT-AS1

Genes in Wide Peak

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

Table S57. 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 14q32.32.

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

Genes
AKT1
TCL1A
TRIP11
GOLGA5
DICER1
TCL6
BCL11B
hsa-mir-203
hsa-mir-4309
hsa-mir-1247
hsa-mir-656
hsa-mir-370
hsa-mir-345
hsa-mir-342
hsa-mir-3173
SERPINA3
BDKRB1
BDKRB2
CALM1
SERPINA6
FOXN3
CHGA
CKB
CRIP1
CRIP2
DIO3
DYNC1H1
EIF5
ELK2AP
EML1
GALC
BRF1
HSP90AA1
IFI27
ITPK1
JAG2
KLC1
MARK3
ATXN3
NDUFB1
SERPINA5
SERPINA1
SERPINA4
PPP2R5C
LGMN
PSMC1
MOK
SEL1L
TNFAIP2
TRAF3
VRK1
WARS
XRCC3
YY1
GPR68
GPR65
ADAM6
DLK1
CCNK
MTA1
RPS6KA5
BAG5
C14orf2
CDC42BPB
TCL1B
KIAA0125
TECPR2
FBLN5
SIVA1
CYP46A1
PAPOLA
PTPN21
RCOR1
PACS2
PPP1R13B
FLRT2
KIF26A
C14orf109
PRO1768
GPR132
SERPINA10
GLRX5
EVL
C14orf129
CINP
ASB2
CPSF2
KCNK10
CDCA4
C14orf102
ATG2B
UBR7
MEG3
SMEK1
BTBD7
TDP1
ZNF839
SPATA7
KCNK13
C14orf132
DDX24
UNC79
BEGAIN
PPP4R4
MOAP1
DIO3OS
INF2
OTUB2
ZFYVE21
MEG8
WDR25
LINC00341
CLMN
CATSPERB
ZC3H14
RIN3
C14orf159
TMEM121
AMN
IFI27L2
SETD3
APOPT1
HHIPL1
C14orf142
STON2
FAM181A
BTBD6
EFCAB11
EXOC3L4
WDR20
AHNAK2
TRMT61A
TDRD9
ANKRD9
AK7
IFI27L1
C14orf79
PLD4
ADSSL1
TTC8
TC2N
SLC24A4
SLC25A29
DEGS2
LINC00239
LOC145216
GSC
SERPINA12
PRIMA1
TTC7B
C14orf49
EML5
MGC23270
NUDT14
LINC00521
SERPINA11
LOC283585
LOC283587
FAM181A-AS1
SNHG10
C14orf177
SLC25A47
LINC00523
KIAA0284
C14orf80
CCDC85C
ITPK1-AS1
SERPINA9
LINC00226
LINC00221
COX8C
ASPG
SERPINA13
C14orf64
RTL1
TMEM179
LOC400236
LOC400238
DICER1-AS1
C14orf180
MIR127
MIR134
MIR136
MIR154
MIR203
MIR299
CCDC88C
MIR323A
MIR337
MIR345
MIR376C
MIR369
MIR376A1
MIR377
MIR379
MIR380
MIR381
MIR382
MIR433
MIR431
MIR329-1
MIR329-2
MIR323B
MIR409
MIR412
MIR410
MIR376B
MIR485
MIR493
MIR432
MIR494
MIR495
MIR496
MIR487A
TEX22
MIR539
MIR376A2
MIR487B
SCARNA13
SNORA28
MIR411
MIR654
MIR655
MIR656
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
SNORA11B
MIR300
MIR541
MIR665
MIR543
MIR889
ZBTB42
LOC100129345
LOC100131366
MIR1247
MIR1185-1
MIR1185-2
MIR1197
MIR1193
MIR4309
MIR3173
LOC100507043
MIR3545
MIR4710
MIR2392

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p24.1.

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

Genes
TGFBR2
RBMS3

Genes in Wide Peak

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

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

Genes
CARS
FANCF
HRAS
LMO1
NUP98
hsa-mir-610
hsa-mir-3159
hsa-mir-4299
hsa-mir-302e
hsa-mir-483
hsa-mir-675
hsa-mir-4298
hsa-mir-210
ADM
AP2A2
AMPD3
APBB1
RHOG
ARNTL
ART1
ASCL2
BDNF
CALCA
CALCB
CCKBR
CD81
CD151
CDKN1C
TPP1
CNGA4
COPB1
CTSD
DRD4
DUSP8
EIF4G2
GAS2
GTF2H1
HBB
HBBP1
HBD
HBE1
HBG1
HBG2
HPX
IGF2
ILK
INS
IRF7
KCNC1
KCNJ11
KCNQ1
LDHA
LDHC
LSP1
MUC2
MUC6
MYOD1
NAP1L4
NELL1
NUCB2
SLC22A18
SLC22A18AS
PDE3B
PIK3C2A
POLR2L
PSMA1
PSMD13
PTH
RNH1
MRPL23
RPL27A
RPLP2
RPS13
RRM1
SAA1
SAA2
SAA3P
SAA4
SCT
SMPD1
TRIM21
ST5
STIM1
ABCC8
TAF10
TALDO1
TEAD1
TH
TSPAN4
TNNI2
TNNT3
TPH1
TRPC2
TSG101
PHLDA2
TUB
WEE1
ZNF143
ZNF195
ZNF214
ZNF215
RASSF7
CSRP3
BBOX1
PPFIBP2
IFITM1
OR6A2
DCHS1
EIF3F
BRSK2
SLC6A5
MICAL2
CTR9
TRIM66
TSPAN32
TSSC4
USH1C
PRMT3
MRVI1
TRIM22
IFITM3
SPON1
DEAF1
IPO7
HTATIP2
IFITM2
TRIM3
OR7E14P
OR7E12P
LYVE1
C11orf58
KCNQ1OT1
PKP3
HPS5
RRAS2
SWAP70
DENND5A
RRP8
SIRT3
OR52A1
ARFIP2
SERGEF
OR5E1P
OR10A3
FXC1
DKK3
RBMXL2
PGAP2
C11orf21
TRPM5
UBQLN3
RNF141
IGF2-AS1
BET1L
CEND1
CYB5R2
TRIM34
CDHR5
TOLLIP
ZDHHC13
USP47
TRIM68
UEVLD
LIN7C
LGR4
PIDD
KCNQ1DN
SOX6
PARVA
MMP26
AKIP1
C11orf16
TMEM9B
NRIP3
ASCL3
CHRNA10
SLC17A6
PNPLA2
PHRF1
SCUBE2
ZBED5
SIGIRR
RIC8A
MRPL17
ANO3
EPS8L2
STK33
CHID1
OR51G1
OR51B4
OR51B2
OR52N1
RIC3
E2F8
SLC25A22
ATHL1
OR51G2
OR51E2
PTDSS2
MOB2
SBF2
KIF18A
FAM160A2
FAR1
BTBD10
PTPN5
MICALCL
TRIM5
NAV2
SYT8
CCDC34
PRKCDBP
SAAL1
ODF3
OSBPL5
LRRC56
MRGPRE
ART5
MRGPRX2
MRGPRX3
MRGPRX4
TRIM78P
TRIM6
OR52E2
OR52J3
OR51L1
OR51A7
OR51S1
OR51F2
OR52R1
OR52M1
OR52K2
OR5P2
OR5P3
CYP2R1
DBX1
OR2D3
OR2D2
OR52W1
OR56A4
OR56A1
SYT9
OR52B4
C11orf40
OR52I2
OR51E1
UBQLNL
MUC15
LOC143666
PLEKHA7
SPTY2D1
TMEM86A
OR10A5
OR2AG1
DNHD1
SCGB1C1
SLC5A12
LDHAL6A
C11orf42
NLRP6
NS3BP
METTL15
OR56B4
ANO5
LOC255512
OR52B2
C11orf35
OR51F1
SVIP
MRGPRX1
OR51B5
KRT8P41
LOC283104
CSNK2A1P
OR51V1
H19
EFCAB4A
TMEM80
IGSF22
OR10A4
OLFML1
LOC283299
C11orf36
NLRP10
NLRP14
ANO9
LUZP2
LOC338651
B4GALNT4
OR52L1
OR2AG2
OR52B6
OR10A2
OVCH2
PDDC1
GALNTL4
B7H6
MRGPRG
KRTAP5-1
KRTAP5-3
KRTAP5-4
IFITM5
FAM99A
OR56B1
GVINP1
INSC
FIBIN
OR52K1
OR52I1
OR51D1
OR52A5
OR51B6
OR51M1
OR51Q1
OR51I1
OR51I2
OR52D1
OR52H1
OR52N4
OR52N5
OR52N2
OR52E6
OR52E8
OR52E4
OR56A3
OR56A5
OR10A6
NAV2-AS4
OR51T1
OR51A4
OR51A2
IFITM10
MIR210
KRTAP5-5
KRTAP5-2
KRTAP5-6
TMEM41B
LOC440028
TRIM6-TRIM34
LOC494141
BDNF-AS1
MIR483
SNORA3
SNORA52
LOC644656
RASSF10
LOC650368
LOC653486
SNORA23
SNORA45
SNORA54
SNORD97
MIR610
INS-IGF2
MUC5B
LOC729013
MIR675
LOC100126784
MRVI1-AS1
FAM99B
LOC100133161
MRPL23-AS1
MIR4298
MIR4299
MTRNR2L8
LOC100500938
MIR210HG
LOC100506305
LOC100506540
SAA2-SAA4
MIR4486
MIR4686
MIR4485
MIR4694
MIR4687

Genes in Wide Peak

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

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

Genes
hsa-mir-1274b
A1BG
FKBP1AP1
PEG3
RPS5
AURKC
ZNF8
ZNF17
MZF1
ZNF132
ZNF134
ZNF135
ZNF154
UBE2M
ZNF264
TRIM28
ZNF256
ZNF211
TRAPPC2P1
ZNF274
ZNF460
SLC27A5
ZIM2
ZNF324
CHMP2A
ZNF544
ZNF586
ZNF416
ZNF446
VN1R1
ZNF304
USP29
ZSCAN18
MGC2752
ZNF329
ZNF419
ZNF552
ZNF671
ZNF606
ZBTB45
ZNF587
ZNF551
ZNF835
ZIM3
ZNF837
ZNF543
C19orf18
ZNF418
ZNF417
ZNF548
ZNF497
ZNF550
ZNF584
ZSCAN4
ZNF549
ZNF547
ZIK1
ZNF776
ZSCAN1
ZSCAN22
ZNF530
ZNF773
ZNF749
ZNF324B
ZNF805
ZNF772
A1BG-AS1
DUXA
LOC646862
ZNF814
MIMT1
LOC100128398
LOC100131691
PEG3-AS1
ZNF587B
MIR4754

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 18q21.2.

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

Genes
SMAD4
ME2
MEX3C
ELAC1
MRO
LOC100287225

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q12.1.

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

Genes
CYLD
hsa-mir-138-2
hsa-mir-3181
hsa-mir-1826
ADCY7
AMFR
BBS2
CBLN1
CES1
GNAO1
MMP2
MT1A
MT1B
MT1E
MT1F
MT1G
MT1H
MT1JP
MT1M
MT1L
MT1X
MT2A
MT3
PHKB
RBL2
SALL1
SIAH1
SLC6A2
SLC12A3
N4BP1
NUP93
IRX5
DNAJA2
ZNF267
NUDT21
ZNF423
RPGRIP1L
ORC6
TP53TG3
DKFZP434H168
TOX3
BRD7
CES1P1
LPCAT2
HEATR3
OGFOD1
VPS35
NOD2
PAPD5
AKTIP
FTO
IRX6
IRX3
SHCBP1
CHD9
ITFG1
NETO2
LONP2
CAPNS2
MT4
GPT2
ABCC11
NKD1
MYLK3
ABCC12
C16orf78
ANKRD26P1
SNX20
LOC146481
CES5A
CNEP1R1
LOC283856
LOC283914
MT1DP
SLC6A10P
C16orf87
LOC388276
LOC390705
CES1P2
FLJ26245
MIR138-2
HERC2P4
UBE2MP1
LOC643714
LOC643802
CRNDE
MT1IP
LINC00273
TP53TG3C
LOC729264
TP53TG3B
LOC100130700
MIR3935
LOC100505619
LOC100507577
MIR548AE2

Genes in Wide Peak

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

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

Genes
BUB1B
PML
TCF12
FLJ27352
C15orf55
hsa-mir-549
hsa-mir-184
hsa-mir-4313
hsa-mir-631
hsa-mir-630
hsa-mir-629
hsa-mir-4312
hsa-mir-4311
hsa-mir-1272
hsa-mir-422a
hsa-mir-190
hsa-mir-2116
hsa-mir-628
hsa-mir-1266
hsa-mir-147b
hsa-mir-1282
hsa-mir-627
hsa-mir-4310
hsa-mir-626
hsa-mir-1233-2
hsa-mir-1233-1
hsa-mir-211
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
ACTC1
ADAM10
ANXA2
APBA2
AQP9
B2M
BBS4
BCL2A1
NBEAP1
BNIP2
CA12
CAPN3
CHRM5
CHRNA3
CHRNA5
CHRNA7
CHRNB4
CKMT1B
CLK3
CRABP1
CSK
CSPG4
CTSH
CYP1A1
CYP1A2
CYP11A1
CYP19A1
DUT
EPB42
ETFA
FAH
FBN1
FGF7
GABPB1
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
GTF2A2
HDC
HEXA
ONECUT1
IDH3A
IL16
IPW
IREB2
ISLR
ITPKA
IVD
LIPC
LOXL1
LTK
SMAD3
SMAD6
MAN2C1
MAP1A
MEIS2
MFAP1
TRPM1
MPI
MYO1E
MYO5A
MYO9A
NDN
NEDD4
NEO1
OAZ2
OCA2
PKM2
PLCB2
PPIB
MAPK6
MAP2K1
MAP2K5
PSMA4
PTPN9
RAB27A
RAD51
RASGRF1
RCN2
RORA
RPL4
RPLP1
RPS17
RYR3
SCG5
SLC12A1
SNRPN
SNX1
SORD
SPINT1
SRP14
THBS1
TJP1
TLE3
TP53BP1
TPM1
TYRO3
TYRO3P
UBE3A
MKRN3
SLC30A4
PAR5
ANP32A
SEMA7A
CILP
PIAS1
EIF3J
JMJD7-PLA2G4B
RAB11A
SNAP23
ALDH1A2
HERC2
HERC1
SNURF
PSTPIP1
USP8
CCNB2
SLC28A2
SLC24A1
CCPG1
GCNT3
COPS2
TRIP4
TGM5
COX5A
STOML1
PIGB
KIF23
IGDCC3
PPIP5K1
AQR
SECISBP2L
KIAA0101
ARHGAP11A
LCMT2
ARNT2
USP3
SLC12A6
NR2E3
BCL2L10
HCN4
SCAMP2
SNUPN
PDCD7
TSPAN3
FEM1B
RASGRP1
SERF2
DENND4A
SNAPC5
HMG20A
CORO2B
CIB2
MTHFS
ARID3B
GNB5
ARPP19
CLPX
MORF4L1
SLC27A2
ADAMTS7
GPR176
CHP
OIP5
ITGA11
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
ZNF609
TBC1D2B
RTF1
MESDC2
CYFIP1
ACSBG1
KIAA1024
MGA
DMXL2
VPS39
FAM189A1
TMED3
AP4E1
CCNDBP1
DAPK2
EID1
C15orf2
C15orf63
ARIH1
SIN3A
TMEM87A
ULK3
RPAP1
GLCE
DKFZP434L187
PYGO1
PLDN
FBXO22
GREM1
NPTN
FOXB1
RPUSD2
TUBGCP4
SCG3
TMOD3
TMOD2
EHD4
SCAPER
DUOX2
MYEF2
RPS27L
NDUFAF1
RSL24D1
NUSAP1
TMEM85
RASL12
SPG21
SPTBN5
PTPLAD1
CTDSPL2
KLF13
RAB8B
DUOX1
CSNK1G1
ZFAND6
MAGEL2
DLL4
INO80
FAM63B
RNF111
ZNF280D
TRPM7
VPS13C
LRRC49
PAQR5
PPP1R14D
DPP8
MTMR10
RPP25
COMMD4
PARP16
TIPIN
CLN6
ZNF770
ZWILCH
FLJ10038
UACA
HAUS2
FAM82A2
DNAJC17
IMP3
LARP6
MNS1
DNAJA4
NOP10
GOLGA6B
MYO5C
NDNL2
FAM214A
C15orf24
C15orf39
THAP10
PAK6
PARP6
DTWD1
CASC5
AVEN
C15orf17
ATP10A
KIAA1199
GJD2
STARD9
ISLR2
VPS18
IGDCC4
SQRDL
FAM108C1
MESDC1
PPCDC
CELF6
STRA6
ZFP106
IQCH
ISL2
RFX7
SPATA5L1
CHAC1
NOX5
EFTUD1
NEIL1
NARG2
AAGAB
LMAN1L
C15orf29
SLTM
PEAK1
SNX22
THSD4
ATP8B4
WDR76
TMEM62
SEMA6D
ANP32A-IT1
C15orf34
PIF1
CCDC33
EDC3
AGSK1
SPG11
ELL3
PLEKHO2
WDR61
CD276
STARD5
POLR2M
C15orf44
NIPA2
C15orf5
ADPGK
APH1B
TLN2
FAM96A
MEX3B
C15orf48
MEGF11
C15orf41
SPPL2A
LINGO1
ZFYVE19
CGNL1
FRMD5
UBL7
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
LOC91450
CALML4
LDHAL6B
UBE2Q2
CHST14
CASC4
LACTB
TUBGCP5
DIS3L
TGM7
CATSPER2
LEO1
SENP8
MTFMT
OSTBETA
HIGD2B
C15orf27
NIPA1
AGPHD1
PLA2G4E
TRIM69
PAR1
C15orf43
LOC145663
C2CD4A
FAM81A
GCOM1
LOC145783
LOC145837
LOC145845
C15orf61
TMCO5A
NRG4
ZSCAN29
TTBK2
CDAN1
STRC
C15orf26
TBC1D21
DYX1C1
CSNK1A1P1
OTUD7A
SPRED1
ODF3L1
PGBD4
ADAL
EXD1
FSIP1
RHOV
SCAMP5
C15orf33
CT62
GRAMD2
MGC15885
LCTL
UBR1
PATL2
SPESP1
LOC253044
LPCAT4
PLA2G4F
LRRC57
LYSMD2
WDR72
SNX33
HMGN2P46
SLC24A5
PRTG
LOC283663
LINC00277
C15orf60
LOC283683
C15orf37
LOC283688
OR4N4
LOC283710
FAM154B
LOC283731
FAM98B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
FBXL22
SNORD108
SNORD109A
SNORD109B
SNORD115-1
TMEM202
WHAMMP3
POTEB
GLDN
GOLGA6A
TMC3
FMN1
SNORD64
PAR4
PAR-SN
RBPMS2
ANKDD1A
LOC348120
MRPL42P5
USP50
TEX9
C15orf52
TNFAIP8L3
C2CD4B
C15orf59
GOLGA8E
OR4M2
OR4N3P
KBTBD13
UBAP1L
SKOR1
ANKRD34C
LOC390660
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
ST20
DUOXA2
MIR184
MIR190A
MIR211
C15orf50
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
UNC13C
LOC440288
GOLGA6L9
LOC440297
LOC503519
CKMT1A
CPLX3
SNORD16
SNORD18A
SNORD18B
SNORD18C
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
LOC645752
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
SH2D7
LOC646938
GOLGA6L10
LOC653061
LOC653075
GOLGA6C
GOLGA6D
HSP90AB4P
SCARNA14
FBXO22-AS1
MIR549
MIR626
MIR627
MIR628
MIR629
MIR630
MIR631
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727849
LOC727924
LOC728758
OIP5-AS1
LOC729739
GOLGA8C
LOC729911
PWRN1
PWRN2
SNORD116-1
SNORD116-2
SNORD116-3
SNORD116-4
SNORD116-5
SNORD116-6
SNORD116-7
SNORD116-8
SNORD116-9
SNORD116-10
SNORD116-11
SNORD116-12
SNORD116-13
SNORD116-14
SNORD116-15
SNORD116-16
SNORD116-17
SNORD116-18
SNORD116-20
SNORD116-21
SNORD116-22
SNORD116-23
SNORD116-24
SNORD116-25
SNORD115-2
SNORD116-26
SNORD116-27
SNORD115-3
SNORD115-4
SNORD115-5
SNORD115-6
SNORD115-7
SNORD115-8
SNORD115-9
SNORD115-10
SNORD115-11
SNORD115-12
SNORD115-13
SNORD115-14
SNORD115-15
SNORD115-16
SNORD115-17
SNORD115-18
SNORD115-19
SNORD115-20
SNORD115-21
SNORD115-22
SNORD115-23
SNORD115-25
SNORD115-26
SNORD115-29
SNORD115-30
SNORD115-31
SNORD115-32
SNORD115-33
SNORD115-34
SNORD115-35
SNORD115-36
SNORD115-37
SNORD115-38
SNORD115-39
SNORD115-40
SNORD115-41
SNORD115-42
SNORD115-43
SNORD115-44
SNORD116-28
SNORD116-29
SNORD115-48
SNORD115-24
SNORD115-27
SNORD115-28
SNORD115-45
SNORD115-47
MIR147B
DNM1P35
LOC100128714
LOC100129387
LOC100130855
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
LOC100132724
GOLGA8DP
UBE2Q2P3
UBE2Q2P2
JMJD7
PLA2G4B
LOC100287559
LOC100287616
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1272
MIR1266
MIR1282
LOC100306975
MIR548H4
MIR2116
MIR1233-2
MIR4311
MIR4312
MIR4310
MIR4313
MIR3942
RPS17L
LOC100505648
LOC100506686
LOC100507466
ST20-MTHFS
SERF2-C15ORF63
DYX1C1-CCPG1
MIR4514
MIR4513
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4716
MIR4713
MIR4511
MIR4509-3
MIR4712
MIR4715
TMCO5B
MYZAP

Genes in Wide Peak

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

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

Genes
hsa-mir-1299
ALDH1B1
PGM5
SHB
ZNF658
FAM75A7
CNTNAP3
ANKRD20A1
FAM201A
CBWD5
ANKRD18A
LOC286297
FOXD4L3
IGFBPL1
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 6q12.

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

Genes
PRDM1
hsa-mir-587
hsa-mir-2113
hsa-mir-4282
hsa-mir-30a
hsa-mir-30c-2
AIM1
AMD1
BAI3
BCKDHB
CCNC
CGA
CNR1
COL9A1
COL12A1
COL19A1
COX7A2
EEF1A1
EPHA7
FOXO3
FYN
GABRR1
GABRR2
GPR6
GRIK2
HDAC2
HTR1B
HTR1E
IMPG1
LAMA4
MARCKS
ME1
MYO6
NT5E
PGM3
POU3F2
PREP
REV3L
RNY4
SIM1
SMPD2
ELOVL4
MAP3K7
NR2E1
TPBG
TTK
DDO
SNX3
RNGTT
CD164
WISP3
WASF1
TBX18
HMGN3
FHL5
ATG5
ZBTB24
SNAP91
FIG4
CASP8AP2
SYNCRIP
SLC35A1
FUT9
TRAF3IP2
PNRC1
ASCC3
BVES
SEC63
KIAA1009
ANKRD6
RIMS1
DOPEY1
ZNF292
CDK19
MDN1
UFL1
PHF3
ORC3
MTO1
PNISR
IBTK
SENP6
FBXL4
SLC17A5
SNORD50A
FILIP1
SESN1
OSTM1
NDUFAF4
CYB5R4
TUBE1
C6orf203
CDC40
UBE2J1
COQ3
PHIP
SOBP
AKIRIN2
QRSL1
AKIRIN2-AS1
DDX43
FAM46A
TMEM30A
LMBRD1
KCNQ5
RARS2
PDSS2
C6orf162
LYRM2
SNX14
HACE1
FAM135A
BEND3
RRAGD
PRDM13
BACH2
SMAP1
C6orf164
POPDC3
MICAL1
OGFRL1
MANEA
LINC00472
KHDC1
GPR63
SPACA1
SH3BGRL2
ARMC2
RPF2
MCHR2
FAXC
GJA10
RTN4IP1
USP45
SLC22A16
C6orf7
UBE2CBP
KIAA1919
GTF3C6
MRAP2
RWDD2A
KLHL32
MB21D1
SLC16A10
RIPPLY2
IRAK1BP1
B3GAT2
C6orf57
CD109
PM20D2
SRSF12
C6orf221
C6orf165
BVES-AS1
PRSS35
LCA5
C6orf163
CCDC162P
AKD1
HS3ST5
LACE1
MMS22L
SCML4
CEP57L1
PPIL6
LOC285758
FLJ34503
DPPA5
EYS
GJB7
SNHG5
C6orf147
LINC00222
LIN28B
MIR30A
MIR30C2
OOEP
MCART3P
GSTM2P1
RFPL4B
C6orf225
TSG1
TRAF3IP2-AS1
SNORD50B
LOC728012
C6orf186
KHDC1L
LOC100130890
LOC100288198
MIR2113
MIR548H3
LOC100422737
MIR4282
LOC100506804
MIR4464
MIR4643

Genes in Wide Peak

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

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

Genes
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
PTPRR
PXMP2
PXN
RAN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
SNRPF
SYT1
TBX5
TBX3
HNF1A
TDG
TSPAN8
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UBE2N
UNG
ZNF10
ZNF26
ZNF84
ZNF140
ALX1
CDK2AP1
BRAP
ULK1
EEA1
RASAL1
PPFIA2
LGR5
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
RAB21
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
TMEM19
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
TBC1D15
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
THAP2
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
TPH2
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
ZFC3H1
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
MRS2P2
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

Arm-level results

Table 3. Get Full Table Arm-level significance table - 27 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.12 | -0.541 | 1 | 0.14 | 0.43 | 0.636
1q | 1955 | 0.23 | 4.17 | 8.82e-05 | 0.11 | -1.64 | 1
2p | 924 | 0.20 | -1.28 | 1 | 0.05 | -6.52 | 1
2q | 1556 | 0.16 | -0.819 | 1 | 0.07 | -4.29 | 1
3p | 1062 | 0.18 | -0.813 | 1 | 0.75 | 21.3 | 0
3q | 1139 | 0.53 | 11.5 | 0 | 0.40 | 5.87 | 1.08e-08
4p | 489 | 0.13 | -3.99 | 1 | 0.44 | 6.21 | 1.51e-09
4q | 1049 | 0.12 | -3.56 | 1 | 0.34 | 4.64 | 6.89e-06
5p | 270 | 0.36 | 2.49 | 0.0283 | 0.21 | -2.26 | 1
5q | 1427 | 0.12 | -2.44 | 1 | 0.39 | 8.24 | 1.48e-15
6p | 1173 | 0.15 | -2.36 | 1 | 0.18 | -1.1 | 1
6q | 839 | 0.11 | -4.77 | 1 | 0.18 | -2.26 | 1
7p | 641 | 0.37 | 4.17 | 8.82e-05 | 0.11 | -4.59 | 1
7q | 1277 | 0.26 | 2.16 | 0.0623 | 0.14 | -2.48 | 1
8p | 580 | 0.33 | 1.93 | 0.0893 | 0.56 | 10.5 | 0
8q | 859 | 0.61 | 14.3 | 0 | 0.20 | -1.07 | 1
9p | 422 | 0.30 | 0.821 | 0.549 | 0.47 | 6.57 | 1.73e-10
9q | 1113 | 0.29 | 2.74 | 0.0153 | 0.26 | 1.52 | 0.143
10p | 409 | 0.09 | -5.78 | 1 | 0.34 | 2.27 | 0.036
10q | 1268 | 0.08 | -4.53 | 1 | 0.24 | 1.55 | 0.141
11p | 862 | 0.14 | -3.24 | 1 | 0.30 | 2.32 | 0.0341
11q | 1515 | 0.18 | -0.0994 | 1 | 0.35 | 6.73 | 6.94e-11
12p | 575 | 0.32 | 2.04 | 0.0748 | 0.13 | -4.38 | 1
12q | 1447 | 0.18 | -0.198 | 1 | 0.08 | -4.11 | 1
13q | 654 | 0.18 | -2.54 | 1 | 0.37 | 4.22 | 4.41e-05
14q | 1341 | 0.32 | 5.02 | 2.08e-06 | 0.14 | -1.98 | 1
15q | 1355 | 0.19 | -0.155 | 1 | 0.24 | 1.67 | 0.119
16p | 872 | 0.22 | -0.466 | 1 | 0.13 | -3.93 | 1
16q | 702 | 0.23 | -0.714 | 1 | 0.16 | -3.14 | 1
17p | 683 | 0.16 | -3.03 | 1 | 0.25 | -0.0448 | 0.942
17q | 1592 | 0.18 | 0.325 | 0.932 | 0.08 | -3.72 | 1
18p | 143 | 0.26 | -1.09 | 1 | 0.31 | 0.457 | 0.636
18q | 446 | 0.15 | -3.47 | 1 | 0.48 | 7.76 | 4.33e-14
19p | 995 | 0.10 | -4.57 | 1 | 0.24 | 0.577 | 0.594
19q | 1709 | 0.15 | -0.827 | 1 | 0.21 | 2.03 | 0.0612
20p | 355 | 0.43 | 5.26 | 7.11e-07 | 0.22 | -1.93 | 1
20q | 753 | 0.42 | 6.52 | 4.69e-10 | 0.15 | -3.1 | 1
21q | 509 | 0.12 | -4.62 | 1 | 0.40 | 4.8 | 3.46e-06
22q | 921 | 0.26 | 0.966 | 0.514 | 0.20 | -1.3 | 1
Xq | 1312 | 0.22 | 0.899 | 0.527 | 0.25 | 1.93 | 0.0721

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/HNSC/1668880/2.GDAC_MergeDataFiles.Finished/HNSC.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 288 Input Tumor Samples.

Tumor Sample Names
TCGA-BA-4074-01A-01D-1432-01
TCGA-BA-4075-01A-01D-1432-01
TCGA-BA-4076-01A-01D-1432-01
TCGA-BA-4077-01B-01D-1432-01
TCGA-BA-4078-01A-01D-1432-01
TCGA-BA-5149-01A-01D-1510-01
TCGA-BA-5151-01A-01D-1432-01
TCGA-BA-5152-01A-02D-1869-01
TCGA-BA-5153-01A-01D-1432-01
TCGA-BA-5555-01A-01D-1510-01

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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