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 2.0.16 (cga svn revision 38839).

Summary

There were 288 tumor samples used in this analysis: 23 significant arm-level results, 28 significant focal amplifications, and 50 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 | 3.7609e-153 | 3.7609e-153 | chr11:70075367-70236792 | 3
7p11.2 | 7.318e-28 | 7.318e-28 | chr7:55046541-55390511 | 1
3q26.33 | 1.1908e-12 | 1.1908e-12 | chr3:180840453-183016018 | 9
8p11.23 | 2.1295e-10 | 2.3199e-10 | chr8:38147031-38270604 | 3
12q15 | 6.0382e-08 | 6.0382e-08 | chr12:69705196-69804210 | 2
9p13.3 | 1.9489e-08 | 1.9468e-07 | chr9:35438295-36015652 | 27
13q22.1 | 2.7942e-06 | 4.2651e-06 | chr13:73865469-73880679 | 0 [KLF5]
2q31.2 | 6.9601e-06 | 2.7867e-05 | chr2:178072000-178247860 | 6
9p22.3 | 5.0053e-07 | 3.6104e-05 | chr9:13397807-14321078 | 3
7q21.3 | 3.6445e-05 | 3.6445e-05 | chr7:91373233-94421450 | 31
17q12 | 3.6445e-05 | 3.6445e-05 | chr17:37658857-37959597 | 12
8q24.21 | 1.7562e-05 | 3.6842e-05 | chr8:128153806-128440166 | 1
2q11.2 | 3.6445e-05 | 0.00011153 | chr2:97507482-97560912 | 4
18q11.2 | 0.00015087 | 0.00015087 | chr18:20747875-20946198 | 2
20q11.21 | 0.00069864 | 0.00069864 | chr20:29887685-30320705 | 16
18p11.31 | 0.0014852 | 0.0014852 | chr18:2830250-4748590 | 11
11p13 | 0.0012344 | 0.0021504 | chr11:35861175-35879772 | 0 [TRIM44]
12p13.33 | 0.002954 | 0.002954 | chr12:1244226-1291266 | 1
8q11.21 | 0.001954 | 0.0048503 | chr8:49265786-49937472 | 2
6p12.1 | 0.020193 | 0.025573 | chr6:53071691-56795741 | 14
5p12 | 0.035337 | 0.035337 | chr5:43797600-43829650 | 0 [NNT]
14q11.2 | 0.049075 | 0.049075 | chr14:21146585-21711097 | 22
5p15.33 | 0.049928 | 0.049928 | chr5:1019815-1415403 | 9
9p24.1 | 6.9196e-05 | 0.055467 | chr9:4465805-6000194 | 20
6q12 | 0.049928 | 0.060612 | chr6:64264873-64594501 | 3
15q26.3 | 0.17295 | 0.17295 | chr15:90360760-102531392 | 78
11p11.2 | 0.043738 | 0.23107 | chr11:44094622-46890387 | 36
13q34 | 0.12303 | 0.24581 | chr13:101394907-115169878 | 69

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
MIR548K

Genes in Wide Peak

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

Table S2. 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 3q26.33.

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

Genes
SOX2
MCF2L2
ATP11B
LAMP3
DCUN1D1
MCCC1
B3GNT5
SOX2-OT
FLJ46066

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 12q15.

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

Genes
LYZ
YEATS4

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 2q31.2.

Table S7. 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 9p22.3.

Table S8. 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 7q21.3.

Table S9. 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
COL1A2
CYP51A1
GNG11
GNGT1
PEX1
MTERF
TFPI2
SGCE
BET1
PEG10
ANKIB1
SAMD9
CCDC132
GATAD1
CASD1
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 17q12.

Table S10. 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
MIR4728

Genes in Wide Peak

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

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

Genes
POU5F1B

Genes in Wide Peak

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

Table S12. 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 18q11.2.

Table S13. 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 20q11.21.

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

Genes
hsa-mir-3193
BCL2L1
ID1
REM1
HM13
COX4I2
DEFB118
LINC00028
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
PSIMCT-1
MIR3193

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 12p13.33.

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

Genes
ERC1

Genes in Wide Peak

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

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

Genes
SNAI2
EFCAB1

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
DST
GCLC
HCRTR2
TINAG
HMGCLL1
LRRC1
ELOVL5
COL21A1
MLIP
FAM83B
GFRAL
KLHL31
RPS16P5

Genes in Wide Peak

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

Table S19. 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 5p15.33.

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

Genes
SLC6A3
TERT
SLC12A7
CLPTM1L
NKD2
SLC6A19
SLC6A18
MIR4457
MIR4635

Genes in Wide Peak

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

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

Genes
JAK2
CD274
hsa-mir-101-2
MLANA
INSL4
RLN1
RLN2
SLC1A1
RCL1
INSL6
AK3
C9orf68
CDC37L1
C9orf46
KIAA1432
ERMP1
PDCD1LG2
KIAA2026
PPAPDC2
MIR101-2

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
EYS

Genes in Wide Peak

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

Table S23. 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
CHD2
FES
IGF1R
MAN2A2
MEF2A
FURIN
PCSK6
SNRPA1
NR2F2
ST8SIA2
IQGAP1
PRC1
SV2B
AP3S2
SEMA4B
CIB1
CHSY1
SYNM
GABARAPL3
VPS33B
OR4F4
SLCO3A1
NGRN
LINS
MCTP2
SELS
UNC45A
RGMA
TTC23
LRRK1
TM2D3
RCCD1
ARRDC4
LOC91948
TARSL2
LRRC28
ASB7
LYSMD4
PGPEP1L
LOC145820
C15orf32
SPATA8
ADAMTS17
DNM1P46
CERS3
FAM169B
ZNF774
C15orf38
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 11p11.2.

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

Genes
EXT2
CREB3L1
hsa-mir-3160-2
ARHGAP1
CHRM4
CRY2
F2
CD82
LRP4
MDK
DGKZ
CHST1
PEX16
MAPK8IP1
TP53I11
ATG13
CKAP5
PHF21A
SLC35C1
AMBRA1
PRDM11
SYT13
ALX4
ZNF408
ACCS
TSPAN18
GYLTL1B
C11orf94
LOC221122
HARBI1
DKFZp779M0652
SNORD67
MIR3160-2
MIR3160-1
LOC100507401
MIR4688

Genes in Wide Peak

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

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

Genes
ERCC5
hsa-mir-1267
ATP4B
COL4A1
COL4A2
EFNB2
F7
F10
FGF14
GAS6
ING1
LAMP1
LIG4
GRK1
SLC10A2
SOX1
TFDP1
TPP2
CUL4A
IRS2
PROZ
ARHGEF7
CDC16
ITGBL1
TUBGCP3
TNFSF13B
RASA3
MYO16
ATP11A
MCF2L
BIVM
TMCO3
ARGLU1
DCUN1D2
ANKRD10
RAB20
CARKD
PCID2
UPF3A
KDELC1
CARS2
GRTP1
ABHD13
TEX30
ADPRHL1
TEX29
METTL21CP1
SPACA7
METTL21C
NALCN
DAOA
DAOA-AS1
FGF14-IT1
LOC283481
LINC00346
CHAMP1
FAM70B
C13orf35
FLJ44054
CCDC168
FLJ41484
LINC00460
FAM155A
LINC00552
MCF2L-AS1
LOC100506394
BIVM-ERCC5
MIR2681
MIR4705

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 - 50 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 | 7.4668e-107 | 8.017e-100 | chr9:21865498-21997722 | 2
8p23.2 | 1.227e-45 | 1.227e-45 | chr8:2079140-6262191 | 1
4q35.2 | 6.2762e-19 | 3.7124e-16 | chr4:187475875-188227950 | 1
2q22.1 | 8.5354e-22 | 3.6492e-15 | chr2:139655617-143637838 | 1
2q37.2 | 9.135e-15 | 4.4098e-10 | chr2:213401694-243199373 | 285
18q23 | 2.543e-11 | 1.0689e-09 | chr18:67995567-78077248 | 36
13q12.11 | 4.5192e-10 | 7.8613e-09 | chr13:19918156-23755126 | 23
9p24.1 | 2.4803e-16 | 1.4941e-08 | chr9:8310705-12693402 | 1
19p13.3 | 1.8302e-08 | 1.8826e-08 | chr19:1-2715627 | 105
10p11.21 | 5.4589e-08 | 7.6927e-08 | chr10:34059131-35328087 | 1
1p12 | 3.0981e-07 | 3.0981e-07 | chr1:112530734-149879544 | 156
16q23.3 | 1.7748e-06 | 1.8353e-06 | chr16:82159666-83542835 | 4
2q21.2 | 2.6197e-13 | 4.8313e-06 | chr2:133423352-134889663 | 2
7q36.1 | 2.2811e-06 | 1.4556e-05 | chr7:148117946-153767963 | 72
1p36.13 | 1.7555e-05 | 1.7555e-05 | chr1:10687727-18958476 | 117
5q11.2 | 2.9872e-08 | 2.6039e-05 | chr5:58260298-59787985 | 3
11q23.1 | 1.2518e-06 | 6.9764e-05 | chr11:104032904-121324206 | 171
17q25.3 | 0.00021045 | 0.00021724 | chr17:80698053-80902410 | 2
9p13.1 | 3.7351e-05 | 0.00053 | chr9:38619152-71152237 | 50
14q32.32 | 0.00046934 | 0.0011911 | chr14:102823245-103654938 | 10
9q34.3 | 0.0017685 | 0.0018792 | chr9:139376600-139456211 | 4
5q35.2 | 0.002193 | 0.0021081 | chr5:176521457-176731866 | 2
3p12.2 | 0.00027634 | 0.0042609 | chr3:75363575-85012839 | 13
3p14.2 | 4.0567e-05 | 0.0048441 | chr3:61234833-62281357 | 2
3p24.1 | 0.00031592 | 0.0071749 | chr3:30051218-30767809 | 1
18q21.2 | 5.6227e-06 | 0.013045 | chr18:48351671-48920689 | 4
3p21.1 | 0.0011652 | 0.017397 | chr3:53923579-55500153 | 3
14q11.2 | 0.012608 | 0.020311 | chr14:1-32800028 | 181
4q22.1 | 0.0032177 | 0.023439 | chr4:90844993-93240505 | 1
7q31.1 | 0.0031766 | 0.023439 | chr7:110725672-111366370 | 1
6p25.3 | 0.032627 | 0.032557 | chr6:1101324-2250882 | 4
19q13.43 | 0.046015 | 0.045318 | chr19:57359801-59128983 | 71
15q15.1 | 0.078958 | 0.076362 | chr15:1-50569667 | 360
4q31.3 | 9.3191e-05 | 0.084562 | chr4:147358277-183246105 | 128
5q15 | 0.0055188 | 0.10454 | chr5:44813655-119802025 | 307
11q14.1 | 0.10383 | 0.10454 | chr11:78285273-82445609 | 6
11q25 | 0.00024083 | 0.10454 | chr11:105849158-135006516 | 279
13q14.2 | 0.0019108 | 0.10454 | chr13:28022105-73284283 | 199
6q24.2 | 0.10795 | 0.1111 | chr6:139787235-171115067 | 172
22q13.31 | 0.11984 | 0.11891 | chr22:42220107-51304566 | 134
16q12.1 | 0.15877 | 0.15784 | chr16:31772318-64981096 | 137
10q23.31 | 0.17695 | 0.17751 | chr10:39064001-105354255 | 515
21q22.3 | 0.17524 | 0.17751 | chr21:37788929-48129895 | 135
21q21.1 | 0.18757 | 0.18549 | chr21:1-31120843 | 71
10p15.1 | 0.14881 | 0.19195 | chr10:4719797-5197880 | 5
22q11.21 | 0.1894 | 0.19195 | chr22:1-18562887 | 26
12p11.1 | 0.19873 | 0.20146 | chr12:33046522-53901104 | 189
17p11.2 | 0.21694 | 0.20965 | chr17:17913823-36836114 | 256
7q11.22 | 0.093437 | 0.22389 | chr7:50860096-82383530 | 178
5p12 | 0.0018373 | 0.31994 | chr5:41510703-99722097 | 264

Genes in Wide Peak

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

Table S26. 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 S27. 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 S28. 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 2q22.1.

Table S29. 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 2q37.2.

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

Genes
ATIC
ACSL3
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
AAMP
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CRYBA2
CYP27A1
DES
DTYMK
EPHA4
FN1
GBX2
GPC1
GPR35
HDLBP
AGFG1
DNAJB2
HTR2B
SP110
IGFBP2
IGFBP5
IHH
CXCR1
CXCR2
CXCR2P1
INHA
INPP5D
IRS1
KCNJ13
NCL
NDUFA10
SEPT2
NEU2
NPPC
PDCD1
PDE6D
SERPINE2
PPP1R7
PSMD1
PTMA
PTPRN
SNORD20
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
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
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
LOC151171
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
TIGD1
LOC200772
CCDC108
C2orf72
CXXC11
RUFY4
DUSP28
ESPNL
ECEL1P2
LOC348761
C2orf62
RBM44
AQP12A
KLHL30
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
BOK-AS1
MIR1244-3
MIR1244-2
MIR3131
MIR4268
MIR3132
MIR4269
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 18q23.

Table S31. 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 S32. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

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

Genes in Wide Peak

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

Table S33. 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 19p13.3.

Table S34. 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
MADCAM1
SF3A2
PPAP2C
AP3D1
MED16
APC2
ABCA7
UQCR11
SBNO2
HMHA1
SHC2
TIMM13
DAZAP1
FGF22
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
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 10p11.21.

Table S35. 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 1p12.

Table S36. 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 16q23.3.

Table S37. 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 2q21.2.

Table S38. 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 7q36.1.

Table S39. 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 1p36.13.

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

Genes
SDHB
CASP9
TNFRSF8
CLCN6
CLCNKA
CLCNKB
EPHA2
MTOR
MFAP2
MTHFR
NPPA
NPPB
PLOD1
EXOSC10
RSC1A1
SRM
TNFRSF1B
ZBTB17
PRDM2
DHRS3
CROCC
MFN2
ANGPTL7
MAD2L2
PDPN
MASP2
MST1P2
MST1P9
PADI2
CTRC
SPEN
PLEKHM2
KAZN
DNAJC16
ATP13A2
TARDBP
PADI4
C1orf144
FBXO2
FBXO6
HSPB7
UBIAD1
PADI1
CELA2B
PADI3
FBXO42
FBLIM1
CASZ1
TMEM51
ARHGEF10L
VPS13D
NBPF1
NECAP2
RCC2
AGTRAP
PTCHD2
MIIP
CELA2A
PRAMEF1
PRAMEF2
EFHD2
RSG1
AGMAT
ACTL8
DDI2
CROCCP2
IGSF21
KIAA2013
C1orf158
FBXO44
CROCCP3
FHAD1
LRRC38
AADACL3
KLHDC7A
ARHGEF19
C1orf127
C1orf64
C1orf126
SLC25A34
ESPNP
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
PADI6
C1orf187
SPATA21
TMEM82
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PRAMEF4
PRAMEF13
PRAMEF3
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
PRAMEF7
PRAMEF19
PRAMEF20
LOC649330
PRAMEF22
PRAMEF15
PRAMEF16
SNORA59B
SNORA59A
PRAMEF14
FLJ37453
NPPA-AS1
MIR3675
MIR4632

Genes in Wide Peak

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

Table S41. 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 11q23.1.

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

Genes
ATM
CBL
DDX6
DDX10
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
hsa-mir-4301
hsa-mir-34c
ACAT1
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CASP1
CASP4
CASP5
CD3D
CD3E
CD3G
CRYAB
DLAT
DPAGT1
DRD2
FDX1
SLC37A4
GRIA4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPB2
HTR3A
IL10RA
IL18
MCAM
NCAM1
NNMT
NPAT
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
SLN
TAGLN
TECTA
THY1
UPK2
ZBTB16
CUL5
ZNF259
USP2
HTR3B
ZW10
UBE4A
C2CD2L
RBM7
MPZL2
HYOU1
ATP5L
TREH
CEP164
EXPH5
PHLDB1
SIK2
SIK3
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
TIMM8B
SIDT2
TRAPPC4
FXYD6
C11orf71
SLC35F2
RAB39A
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
VPS11
TEX12
TMPRSS4
IFT46
DSCAML1
ARHGAP20
USP28
CARD18
AASDHPPT
ABCG4
C11orf1
RNF26
NLRX1
ALG9
PDZD3
TMPRSS5
MFRP
BCO2
TMPRSS13
KIAA1826
BUD13
TMEM25
DIXDC1
ZC3H12C
ALKBH8
FDXACB1
C11orf52
CARD16
C1QTNF5
APOA5
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
C11orf65
MPZL3
TBCEL
TMEM136
OAF
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
CCDC84
C11orf53
C11orf34
C11orf87
C11orf92
C11orf88
MIR34B
MIR34C
CARD17
LOC643733
LOC643923
CLDN25
LOC649133
RPL23AP64
LOC100132078
LOC100288346
BACE1-AS
MIR4301
LOC100499227
MIR3656
CASP12
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4491
MIR4492
LOC100652768

Genes in Wide Peak

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

Table S43. 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 9p13.1.

Table S44. 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 14q32.32.

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

Genes
hsa-mir-4309
TNFAIP2
TRAF3
CDC42BPB
TECPR2
RCOR1
AMN
EXOC3L4
ANKRD9
MIR4309

Genes in Wide Peak

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

Table S46. 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 5q35.2.

Table S47. 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 3p12.2.

Table S48. 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
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 3p14.2.

Table S49. 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 3p24.1.

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

Genes
TGFBR2

Genes in Wide Peak

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

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

Genes
SMAD4
ME2
MEX3C
ELAC1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p21.1.

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

Genes
CACNA2D3
LRTM1
ESRG

Genes in Wide Peak

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

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

Genes
CCNB1IP1
hsa-mir-624
hsa-mir-3171
hsa-mir-4307
hsa-mir-208b
hsa-mir-1201
ANG
APEX1
ARHGAP5
BCL2L2
CEBPE
CMA1
LTB4R
CTSG
DAD1
COCH
FOXG1
GPR33
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
AP4S1
SUPT16H
ACIN1
SCFD1
KHNYN
SLC7A8
HECTD1
HEATR5A
NGDN
LRP10
TINF2
OR10G3
OR10G2
OR4E2
CIDEB
CHMP4A
STXBP6
STRN3
SLC39A2
FAM158A
ZNF219
GMPR2
SLC22A17
HAUS4
C14orf119
RNF31
RBM23
C14orf167
G2E3
OSGEP
ARHGEF40
METTL3
LTB4R2
SDR39U1
RPGRIP1
NDRG2
NYNRIN
HOMEZ
CHD8
C14orf93
ABHD4
EDDM3B
CDH24
METTL17
IL25
THTPA
OR4K5
OR11H2
OR4K1
IPO4
NUBPL
DCAF11
OR4K15
JPH4
RNASE7
ARHGAP5-AS1
RAB2B
AJUBA
ZFHX2
RPPH1
LRRC16B
PPP1R3E
TMEM55B
TTC5
C14orf126
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
MIR624
DHRS4L1
SNORD126
MIR208B
MIR4307
LOC100505967
LOC100506071
NEDD8-MDP1
BCL2L2-PABPN1
MIR548AI
MIR4707

Genes in Wide Peak

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

Table S54. 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 7q31.1.

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

Genes
LRRN3

Genes in Wide Peak

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

Table S56. 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 19q13.43.

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

Genes
hsa-mir-1274b
A1BG
FKBP1AP1
RPS5
AURKC
ZNF8
ZNF17
MZF1
ZNF132
ZNF134
ZNF135
ZNF154
UBE2M
ZNF264
TRIM28
ZNF256
ZNF211
TRAPPC2P1
ZNF274
ZNF460
SLC27A5
ZNF324
CHMP2A
ZNF544
ZNF586
ZNF416
ZNF446
VN1R1
ZNF304
USP29
ZSCAN18
MGC2752
ZNF329
ZNF419
ZNF552
ZNF671
ZNF606
ZBTB45
ZNF587
ZNF551
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
LOC100128398
LOC100131691
ZNF587B
MIR4754

Genes in Wide Peak

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

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

Genes
BUB1B
C15orf55
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
APBA2
B2M
NBEAP1
CAPN3
CHRM5
CHRNA7
CKMT1B
DUT
EPB42
FBN1
FGF7
GABRA5
GABRB3
GABRG3
GALK2
GANC
GATM
GCHFR
PDIA3
HDC
IPW
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
TRPM1
NDN
OCA2
PLCB2
RAD51
RYR3
SCG5
SLC12A1
SNRPN
SORD
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
SLC30A4
PAR5
EIF3J
JMJD7-PLA2G4B
SNAP23
HERC2
SNURF
SLC28A2
COPS2
TGM5
PPIP5K1
AQR
SECISBP2L
ARHGAP11A
LCMT2
SLC12A6
RASGRP1
SERF2
SLC27A2
GPR176
CHP
OIP5
BAHD1
FAN1
CEP152
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
VPS39
FAM189A1
CCNDBP1
EID1
C15orf2
C15orf63
TMEM87A
RPAP1
DKFZP434L187
PLDN
GREM1
RPUSD2
TUBGCP4
EHD4
DUOX2
MYEF2
NDUFAF1
NUSAP1
TMEM85
SPTBN5
CTDSPL2
KLF13
DUOX1
MAGEL2
DLL4
INO80
PPP1R14D
MTMR10
ZNF770
HAUS2
FAM82A2
DNAJC17
NOP10
NDNL2
C15orf24
PAK6
DTWD1
CASC5
AVEN
ATP10A
GJD2
STARD9
VPS18
SQRDL
ZFP106
SPATA5L1
CHAC1
C15orf29
ATP8B4
WDR76
TMEM62
SEMA6D
SPG11
ELL3
NIPA2
C15orf48
C15orf41
ZFYVE19
FRMD5
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SHF
DUOXA1
SNORD107
CHST14
CASC4
TUBGCP5
TGM7
CATSPER2
NIPA1
PLA2G4E
TRIM69
PAR1
C15orf43
LOC145663
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
C15orf33
UBR1
PATL2
LPCAT4
PLA2G4F
LRRC57
HMGN2P46
SLC24A5
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
SHC4
CTXN2
HERC2P2
C15orf53
C15orf54
DUOXA2
MIR211
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
LOC503519
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
LOC645212
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
MIR626
MIR627
ANP32AP1
SNORD116-19
GOLGA6L6
LOC727924
LOC728758
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
MIR147B
LOC100128714
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
GOLGA8DP
JMJD7
PLA2G4B
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1282
LOC100306975
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4716
MIR4509-3
MIR4715
TMCO5B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q31.3.

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

Genes
FBXW7
hsa-mir-1305
hsa-mir-4276
hsa-mir-548t
hsa-mir-1979
hsa-mir-3140
hsa-mir-548g
AGA
ANXA2P1
LRBA
CLCN3
CPE
CTSO
EDNRA
ETFDH
FGA
FGB
FGG
GK3P
GLRB
GPM6A
GRIA2
GUCY1A3
GUCY1B3
HMGB2
HPGD
NR3C2
NEK1
NPY1R
NPY2R
NPY5R
PET112
PLRG1
POU4F2
PPID
RPS3A
MSMO1
SFRP2
TDO2
TLL1
TLR2
VEGFC
GLRA3
SAP30
SNORD73A
LRAT
HAND2
RAPGEF2
MFAP3L
MAB21L2
ADAM29
ANXA10
KLHL2
SCRG1
PALLD
KIAA0922
TRIM2
ANP32C
FBXO8
ARFIP1
SPOCK3
AADAT
FAM198B
ACCN5
GALNT7
DKFZP434I0714
DCHS2
C4orf27
MARCH1
NEIL3
TMEM144
C4orf43
DDX60
TMEM184C
PDGFC
FSTL5
FNIP2
SH3RF1
RXFP1
SPCS3
ARHGAP10
NBLA00301
MAP9
CEP44
TTC29
MND1
SLC10A7
TKTL2
CBR4
FHDC1
MGC45800
PRMT10
DDX60L
NAF1
WDR17
SPATA4
ASB5
SH3D19
C4orf39
C4orf45
DCLK2
TRIM60
RBM46
C4orf46
TIGD4
TMEM154
TMEM192
LOC285501
RNF175
LOC340017
PRSS48
TRIM61
HSP90AA6P
GALNTL6
MIR578
LINC00290
FAM160A1
MIR1305
MIR3140
MIR4276
MIR3688-1
LOC100505989
LOC100506013
LOC100506085
LOC100506122
MIR4453
MIR4799
MIR3688-2

Genes in Wide Peak

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

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

Genes
APC
IL6ST
PIK3R1
hsa-mir-1244-2
hsa-mir-548f-3
hsa-mir-548p
hsa-mir-583
hsa-mir-2277
hsa-mir-9-2
hsa-mir-4280
hsa-mir-582
hsa-mir-449c
hsa-mir-581
TRIM23
ARSB
BHMT
BTF3
CAMK4
CAST
CCNB1
CCNH
CDK7
CDO1
CETN3
CHD1
CKMT2
ERCC8
AP3S1
COX7C
CRHBP
HAPLN1
VCAN
DMXL1
DHFR
EFNA5
F2R
F2RL1
F2RL2
FER
FOXD1
GLRX
GTF2H2
GZMA
GZMK
HEXB
HMGCR
HSD17B4
HTR1A
ISL1
ITGA1
ITGA2
KCNN2
KIF2A
TNPO1
LNPEP
CD180
MAN2A1
MAP1B
MCC
MEF2C
MAP3K1
MOCS2
MSH3
NAIP
NDUFS4
PAM
PCSK1
PDE4D
PGGT1B
PMCHL2
RAD17
RASA1
RASGRF2
RPS23
SMN1
SMN2
SRP19
TAF9
TBCA
NR2F1
THBS4
XRCC4
ST8SIA4
REEP5
SERF1A
ENC1
AP3B1
PPAP2A
PDE8B
HSPB3
ATG12
NREP
RAB9BP1
HOMER1
SCAMP1
CARTPT
TTC37
ZFYVE16
PJA2
EDIL3
COL4A3BP
LHFPL2
CWC27
CCNO
NSA2
FST
POLR3G
PLK2
IQGAP2
SMA4
SMA5
ESM1
ADAMTS6
RHOBTB3
ELL2
SV2C
MRPS27
PPIP5K2
PPWD1
OTP
SKIV2L2
SSBP2
BHMT2
TNFAIP8
PART1
FAM169A
RNU5E-1
RNU5D-1
DIMT1
DMGDH
TMED7
IPO11
GCNT4
COMMD10
POLK
ERAP1
PELO
DHX29
FLJ11235
DDX4
SGTB
ARL15
GIN1
AGGF1
WDR41
TRIM36
RIOK2
DEPDC1B
BDP1
ERBB2IP
FEM1C
NLN
SEMA6A
ARRDC3
ZSWIM6
ANKRA2
MCCC2
EPB41L4A
CENPK
ERAP2
RGNEF
FBXL17
YTHDC2
SLC30A5
CENPH
GPBP1
PARP8
ANKRD55
MCTP1
PTCD2
ELOVL7
C5orf44
NUDT12
ATG10
SPATA9
TSSK1B
FAM172A
GPR98
UTP15
ZCCHC9
ANKRD32
ZBED3
GFM2
SPZ1
TSLP
C5orf30
SLC25A46
NDUFAF2
MRPS36
ATP6AP1L
SNX18
EPB41L4A-AS1
FCHO2
RAB3C
LYSMD3
C5orf35
IL31RA
EMB
SLCO6A1
JMY
POU5F2
TMEM171
TMEM174
POC5
STARD4
WDR36
ACOT12
SREK1
SLC38A9
TMEM167A
MBLAC2
TMEM161B
MARVELD2
ARSK
FAM81B
CCDC112
MIER3
CDC20B
PAPD4
DCP2
LIX1
ZNF366
FAM151B
S100Z
CCDC125
C5orf27
GAPT
CMYA5
AQPEP
ANKRD31
SERINC5
LOC257396
KIAA0825
GPR150
DTWD2
NBPF22P
C5orf64
RNF180
SREK1IP1
RGMB
RFESD
FAM170A
ANKRD34B
IDAS
ACTBL2
FAM174A
MTX3
HCN1
SLCO4C1
TICAM2
MAST4
RNF138P1
RGS7BP
MIR9-2
CRSP8P
FLJ42709
GPX8
FLJ35946
MIR449A
LOC642366
TMEM232
C5orf43
LOC644100
LOC644936
LINC00461
LOC647859
GUSBP3
GTF2H2B
SNORA13
SCARNA18
SNORA47
MIR449B
MIR581
MIR583
GTF2H2C
LOC728342
SERF1B
LOC728723
GTF2H2D
GUSBP9
LOC100129716
LRRC70
LOC100131067
FAM159B
LOC100133050
LOC100170939
LOC100272216
LOC100289230
LOC100289673
MIR1244-1
TMED7-TICAM2
NCRUPAR
LOC100303749
MIR2277
MIR449C
MIR1244-3
MIR1244-2
MIR4280
MTRNR2L2
MIR3607
MIR3660
LOC100505678
LOC100505894
OCLN
MIR4804
MIR3977
MIR4803

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q14.1.

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

Genes
hsa-mir-4300
hsa-mir-708
ODZ4
FAM181B
MIR708
MIR4300

Genes in Wide Peak

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

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

Genes
ATM
CBL
DDX6
DDX10
FLI1
MLL
PAFAH1B2
POU2AF1
SDHD
PCSK7
ARHGEF12
hsa-mir-3167
hsa-mir-100
hsa-mir-4301
hsa-mir-34c
ACAT1
ACRV1
APLP2
APOA1
APOA4
APOC3
ARCN1
FXYD2
CXCR5
CD3D
CD3E
CD3G
CHEK1
CRYAB
DLAT
DPAGT1
DRD2
ETS1
FDX1
SLC37A4
GRIK4
GUCY1A2
H2AFX
HMBS
HSPA8
HSPB2
HTR3A
IL10RA
IL18
STT3A
KCNJ1
KCNJ5
VWA5A
MCAM
NCAM1
NFRKB
NNMT
NPAT
NRGN
OPCML
PPP2R1B
PTS
PVRL1
RDX
RPS25
SC5DL
SCN2B
SCN4B
ST3GAL4
SLN
SORL1
SRPR
ST14
TAGLN
TECTA
THY1
UPK2
ZBTB16
ZNF202
CUL5
BARX2
ZNF259
USP2
HTR3B
ZW10
UBE4A
EI24
FEZ1
ARHGAP32
C2CD2L
RBM7
MPZL2
HYOU1
ATP5L
ADAMTS8
TREH
CEP164
IGSF9B
EXPH5
PHLDB1
SIK2
NCAPD3
SIK3
VSIG2
BACE1
TRIM29
CADM1
POU2F3
HINFP
REXO2
OR8G2
OR8B8
OR8G1
TIMM8B
OR8B2
ACAD8
B3GAT1
DCPS
ZBTB44
THYN1
DDX25
NTM
CDON
SIDT2
TRAPPC4
SPA17
FXYD6
SIAE
C11orf71
ROBO4
SLC35F2
RAB39A
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
FOXRED1
SCN3B
VPS11
TEX12
CRTAM
TMPRSS4
IFT46
PRDM10
DSCAML1
GRAMD1B
ARHGAP20
USP28
AASDHPPT
PKNOX2
TP53AIP1
ABCG4
ROBO3
C11orf1
RNF26
FAM118B
NLRX1
C11orf61
ALG9
CLMP
PDZD3
C11orf63
CCDC15
TMPRSS5
PUS3
MFRP
JAM3
BCO2
TMPRSS13
KIAA1826
KIRREL3
BUD13
TMEM25
RPUSD4
TBRG1
UBASH3B
DIXDC1
ZC3H12C
GLB1L2
ESAM
ALKBH8
FDXACB1
C11orf52
VPS26B
GLB1L3
TIRAP
C1QTNF5
PANX3
APOA5
TMEM45B
C11orf93
PIH1D2
FAM55A
FAM55B
AMICA1
KBTBD3
CWF19L2
KDELC2
LAYN
TTC36
PATE1
C11orf65
ADAMTS15
MPZL3
C11orf45
HYLS1
TMEM218
SLC37A2
OR8B12
OR8G5
OR10G8
OR10G9
OR10S1
OR6T1
OR4D5
TBCEL
TMEM136
SPATA19
HEPACAM
OAF
ANKK1
RNF214
LOC283143
BCL9L
FOXR1
CCDC153
OR8D1
OR8D2
OR8B4
KIRREL3-AS3
LOC283174
LOC283177
CCDC84
TMEM225
OR8D4
C11orf53
LOC341056
C11orf34
BSX
OR6X1
OR6M1
OR10G4
OR10G7
OR8B3
OR8A1
C11orf87
C11orf92
C11orf88
MIR100HG
PATE2
PATE4
FLJ39051
SNX19
MIRLET7A2
MIR100
MIR125B1
MIR34B
MIR34C
BLID
LINC00167
HEPN1
LOC643923
CLDN25
LOC649133
RPL23AP64
LOC100128239
LOC100132078
PATE3
LOC100288346
BACE1-AS
MIR4301
MIR3167
LOC100499227
MIR3656
LOC100507392
LOC100526771
HSPB2-C11orf52
FXYD6-FXYD2
MIR4697
MIR4493
MIR4491
MIR4492
LOC100652768

Genes in Wide Peak

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

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

Genes
BRCA2
CDX2
FLT3
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
ALOX5AP
ATP7B
RCBTB2
CPB2
DACH1
ELF1
ESD
FOXO1
FLT1
MLNR
GTF2F2
GUCY1B2
HMGB1
HTR2A
PDX1
KPNA3
MAB21L1
SMAD9
NEK3
PCDH8
PCDH9
UBL3
RFC3
RFXAP
ATXN8OS
SLC7A1
TPT1
TRPC4
TNFSF11
SUCLA2
DLEU2
TSC22D1
CCNA1
DCLK1
KL
ITM2B
MTRF1
UTP14C
FRY
LPAR6
SLC25A15
TRIM13
USPL1
MRPS31
DLEU1
N4BP2L2
OLFM4
POSTN
HSPH1
SUGT1
LECT1
WBP4
AKAP11
EXOSC8
FNDC3A
PDS5B
KIAA0564
ZC3H13
SPG20
LRCH1
MTUS2
INTS6
CKAP2
NUFIP1
NBEA
PCDH17
C13orf15
MED4
DNAJC15
ALG5
VPS36
POLR1D
PHF11
POMP
UFM1
SOHLH2
ENOX1
RCBTB1
NUDT15
KIAA1704
FAM48A
THSD1
CYSLTR2
SPRYD7
COG6
KLHL1
PCDH20
NAA16
RNASEH2B
DHRS12
KIAA0226L
PROSER1
TDRD3
CDADC1
CAB39L
DIAPH3
CCDC70
COG3
SETDB2
KATNAL1
KBTBD7
EBPL
C13orf33
KBTBD6
STARD13
N4BP2L1
EPSTI1
ARL11
WDFY2
CG030
LINC00284
CSNK1A1L
RXFP2
TEX26
PRR20A
FAM216B
LACC1
LINC00330
HNRNPA1L2
ST13P4
B3GALTL
DGKH
CCDC122
STOML3
EEF1DP3
GSX1
FAM194B
SPERT
DLEU7
FAM124A
TPTE2P3
CTAGE10P
LNX2
SLC25A30
PAN3
OR7E156P
SUGT1P3
SIAH3
KCNRG
LINC00282
SLC46A3
LINC00550
FREM2
NEK5
THSD1P1
KCTD4
NHLRC3
SERP2
SERTM1
LINC00547
LINC00548
MIR15A
MIR16-1
ATP5EP2
LOC440131
ALG11
TSC22D1-AS1
PRHOXNB
ZAR1L
SERPINE3
SNORA31
MIR621
CCDC169
PRR20B
PRR20C
PRR20D
PRR20E
LINC00426
TPT1-AS1
PAN3-AS1
MIR1297
MIR548F5
MIR759
MIR320D1
MIR4305
MIR3169
MIR3613
OR7E37P
TEX26-AS1
SPG20OS
LOC100507240
LOC100509894
CCDC169-SOHLH2
MIR4703
LOC100616668

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q24.2.

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

Genes
MLLT4
FGFR1OP
hsa-mir-1913
hsa-mir-1202
hsa-mir-1273c
ACAT2
CCR6
ESR1
FUCA2
GPR31
GRM1
HIVEP2
IGF2R
KIF25
LPA
MAS1
MAP3K4
NMBR
OPRM1
PARK2
PCMT1
PDCD2
PLAGL1
PLG
PSMB1
RPS6KA2
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCP1
TCP10
TCTE3
DYNLT1
THBS2
UTRN
EZR
VIP
EPM2A
PEX3
RNASET2
STX11
SYNJ2
LATS1
QKI
WTAP
AKAP12
PHACTR2
UST
PDE10A
RAB32
KATNA1
SCAF8
TAB2
SASH1
SYNE1
MTHFD1L
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
DLL1
MRPL18
CLDN20
NOX3
TFB1M
AIG1
SNX9
VTA1
BRP44L
UNC93A
MTRF1L
RMND1
PHF10
C6orf70
AGPAT4
TULP4
HYMAI
GPR126
PLEKHG1
ARID1B
TMEM181
ZBTB2
SMOC2
ULBP3
C6orf211
ZDHHC14
ADGB
FRMD1
AGPAT4-IT1
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
SF3B5
RSPH3
TTLL2
FBXO30
FAM120B
FNDC1
LRP11
LTV1
SERAC1
PPIL4
LINC00473
SYTL3
SFT2D1
C6orf72
TAGAP
ADAT2
STXBP5
PACRG
RAET1E
LOC153910
ZC2HC1B
CNKSR3
RAET1L
PNLDC1
LOC154449
DACT2
C6orf118
OSTCP1
WDR27
SHPRH
LOC285740
LOC285796
PRR18
ZC3H12D
NUP43
RAET1G
SUMO4
C6orf120
SAMD5
IYD
DKFZp451B082
TCP10L2
LINC00242
GTF2H5
LOC441177
LOC645434
RAET1K
MLLT4-AS1
SNORA20
SNORA29
LOC729176
LOC729178
TMEM242
LOC729603
HGC6.3
LOC100128176
LOC100129518
C6orf99
LOC100132735
LOC100289495
MIR1913
MIR3918
MIR3939
MIR3668
MIR3692
LOC100507489
LOC100507557
CAHM
MIR4466
MIR4465
MIR4644
LOC100652739

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.31.

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

Genes
hsa-mir-3201
hsa-let-7b
hsa-mir-1249
hsa-mir-33a
ACR
ARSA
BIK
TSPO
MPPED1
CHKB
CPT1B
CYP2D7P1
CYP2D6
CYB5R3
TYMP
FBLN1
NAGA
NDUFA6
PPARA
MAPK11
MAPK12
SBF1
SREBF2
TCF20
UPK3A
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
NUP50
RABL2B
PACSIN2
GRAMD4
TTLL12
MLC1
KIAA0930
MAPK8IP2
PLXNB2
BRD1
ARHGAP8
TBC1D22A
TTLL1
SAMM50
ATXN10
FAM19A5
SULT4A1
RIBC2
ARFGAP3
SMC1B
RRP7A
MCAT
PARVB
NCAPH2
GTSE1
A4GALT
MOV10L1
FAM118A
TTC38
C22orf26
MIOX
PRR5
TRMU
SEPT3
PANX2
PARVG
CERK
EFCAB6
CENPM
ALG12
CRELD2
ADM2
SCUBE1
TRABD
PNPLA3
SELO
HDAC10
LDOC1L
POLDIP3
KIAA1644
SHANK3
TUBGCP6
LOC90834
LMF2
C22orf32
RRP7B
SERHL
PHF21B
KLHDC7B
TNFRSF13C
FAM109B
NFAM1
PNPLA5
LOC150381
C22orf40
CN5H6.4
WBP2NL
SERHL2
RNU12
ATP5L2
LOC284933
RPL23AP82
BK250D10.8
LOC339685
C22orf34
CHKB-CPT1B
LOC388906
LINC00207
MIRLET7BHG
FLJ46257
IL17REL
MIRLET7A3
MIRLET7B
MIR33A
LINC00229
FAM116B
PIM3
SHISA8
ODF3B
PRR5-ARHGAP8
SYCE3
LOC730668
LOC100128946
LOC100132273
LOC100144603
LOC100271722
MIR1249
MIR3201
MIR3619
LOC100506714
MIR4763
MIR4762
MIR4535

Genes in Wide Peak

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

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

Genes
CYLD
HERPUD1
hsa-mir-138-2
hsa-mir-3181
hsa-mir-1826
ADCY7
AMFR
BBS2
CBLN1
CDH8
CES1
CETP
CNGB1
CSNK2A2
GNAO1
GOT2
KIFC3
MMP2
MMP15
MT1A
MT1B
MT1E
MT1F
MT1G
MT1H
MT1JP
MT1M
MT1L
MT1X
MT2A
MT3
PHKB
POLR2C
RBL2
SALL1
CCL17
CCL22
CX3CL1
SIAH1
SLC6A2
SLC12A3
GPR56
N4BP1
NUP93
IRX5
DNAJA2
KATNB1
ZNF267
NUDT21
CNOT1
ZNF423
RPGRIP1L
ARL2BP
ORC6
TP53TG3
DKFZP434H168
TOX3
CCDC113
C16orf80
BRD7
PLLP
CES1P1
LPCAT2
HEATR3
SLC38A7
OGFOD1
DOK4
VPS35
COQ9
CIAPIN1
ZNF319
NOD2
PAPD5
AKTIP
GINS3
NDRG4
FTO
IRX6
IRX3
C16orf57
SHCBP1
SETD6
FAM192A
CHD9
ITFG1
NETO2
LONP2
NLRC5
CCDC135
CAPNS2
MT4
GPT2
ABCC11
NKD1
RSPRY1
MYLK3
CCDC102A
ABCC12
C16orf78
ANKRD26P1
SNX20
LOC146481
CPNE2
GPR114
PRSS54
CES5A
GPR97
CNEP1R1
LOC283856
LOC283914
MT1DP
TEPP
SLC6A10P
C16orf87
LOC388276
LOC390705
CES1P2
FLJ26245
MIR138-2
HERC2P4
UBE2MP1
LOC643714
LOC643802
CRNDE
MT1IP
LOC644649
LINC00273
TP53TG3C
SNORA46
SNORA50
LOC729264
TP53TG3B
LOC100130700
MIR3935
LOC100505619
LOC100507577
MIR548AE2

Genes in Wide Peak

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

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

Genes
BMPR1A
TLX1
NFKB2
PRF1
PTEN
RET
NCOA4
SUFU
hsa-mir-1307
hsa-mir-146b
hsa-mir-3158-1
hsa-mir-608
hsa-mir-1287
hsa-mir-607
hsa-mir-3157
hsa-mir-107
hsa-mir-346
hsa-mir-606
hsa-mir-1254
hsa-mir-1296
hsa-mir-548f-1
hsa-mir-605
hsa-mir-4294
hsa-mir-3156-1
ACTA2
ADK
ALOX5
ANXA8L2
ANK3
ANXA2P3
ANXA7
ANXA11
FAS
ARL3
CAMK2G
ENTPD1
CDK1
CHAT
CHUK
ABCC2
COL13A1
COX15
CPN1
CTSL1P2
CYP2C19
CYP2C8
CYP2C9
CYP2C18
CYP17A1
CYP26A1
DNA2
DNTT
EGR2
EIF4EBP2
ERCC6
FGF8
GDF2
GDF10
GLUD1
GOT1
GRID1
HELLS
HHEX
HK1
HNRNPF
HNRNPH3
HPS1
HTR7
IDE
IFIT2
IFIT1
IFIT3
KCNMA1
KIF11
LIPA
MAT1A
MBL2
MSMB
NDUFB8
NODAL
P4HA1
PAX2
PCBD1
PDE6C
PGAM1
PITX3
PLAU
PPA1
PPP1R3C
PPP3CB
PPYR1
SRGN
PRKG1
MAPK8
PSAP
PSD
ALDH18A1
RBP3
RBP4
RGR
RPS24
SCD
CXCL12
SFRP5
SFTPD
FBXW4
SLC18A3
SLIT1
SNCG
SUPV3L1
TACR2
TAF5
TFAM
TLL2
UBE2D1
VCL
VDAC2
WNT8B
ZNF22
ZNF32
ZNF33B
CCDC6
SLC25A16
ZNF239
PARG
NDST2
MBL1P
LIPF
GBF1
LDB1
SGPL1
BTRC
CH25H
PKD2L1
BTAF1
PAPSS2
INA
PDLIM1
NEURL
DDX21
LGI1
NOLC1
DLG5
CHST3
VPS26A
MINPP1
KIF20B
SEC24C
GPRIN2
BMS1
SPOCK2
ZNF518A
RHOBTB1
FRAT1
PPIF
ACTR1A
HNRNPA3P1
NPM3
MICU1
RPP30
SORBS1
ERLIN1
LBX1
NRG3
MGEA5
C10orf116
C10orf10
POLR3A
ZWINT
LDB3
ECD
CPEB3
ZNF365
DKK1
NT5C2
PDCD11
KIAA0913
WAPAL
PPRC1
RRP12
TBC1D12
DNAJC9
DNMBP
CSTF2T
FRAT2
SIRT1
KAT6B
TSPAN15
IFIT5
DPCD
SEC31B
NUDT13
HERC4
PTPN20B
LRIT1
TCTN3
KIAA1279
C10orf12
ANKRD2
CNNM1
MYOF
AP3M1
ANKRD1
GHITM
KIAA1274
C10orf28
POLL
CTNNA3
BLNK
A1CF
NRBF2
KCNIP2
NEUROG3
ASCC1
EXOSC1
MRPS16
CALHM2
CUTC
PLCE1
DUSP13
PANK1
FXYD4
FAM190B
EXOC6
FAM35A
DDIT4
CCNJ
MARCH5
DNAJB12
CNNM2
C10orf26
CRTAC1
CEP55
LRRC20
CWF19L1
SLC29A3
RNLS
PI4K2A
CSGALNACT2
H2AFY2
HIF1AN
RUFY2
FAM178A
FAM21B
CCAR1
OGDHL
CISD1
DNAJC12
ASAH2
C10orf2
SAR1A
TM9SF3
ENTPD7
ZMIZ1
AS3MT
STAMBPL1
WDFY4
SEMA4G
ARHGAP22
MYOZ1
AVPI1
HPSE2
CDH23
PBLD
NPFFR1
C10orf54
MMS19
NOC3L
PCDH15
CUEDC2
DDX50
FBXL15
OR13A1
C10orf76
HPS6
MMRN2
TMEM180
SYNPO2L
C10orf95
PDZD7
UBTD1
BICC1
FAM213A
HKDC1
TET1
TNKS2
TRIM8
TSPAN14
KAZALD1
SFXN3
SLC25A28
ELOVL3
MARVELD1
SYT15
RASSF4
C10orf11
PCGF6
ARID5B
LOXL4
ZDHHC16
C10orf58
DYDC2
PCGF5
LZTS2
PHYHIPL
LCOR
MRPL43
PLA2G12B
MYPN
PYROXD2
USMG5
LOC84856
ZNF503
AIFM2
ADO
ATAD1
ARHGAP19
LOC84989
LINC00263
MCU
CDHR1
OPALIN
ZFAND4
OPN4
HOGA1
C10orf71
CHCHD1
ZMYND17
TTC18
ZNF488
PIK3AP1
MORN4
ZFYVE27
COMTD1
FRA10AC1
ANKRD22
SFXN2
AGAP4
C10orf32
NUDT9P1
AGAP11
CALHM3
ANAPC16
ADAMTS14
C10orf129
SAMD8
LIPJ
CFL1P1
FRMPD2
DYDC1
EIF5AL1
HECTD2
FGFBP3
USP54
NKX2-3
SLC35G1
FAM170B
C10orf128
FUT11
OIT3
LOC170425
ANTXRL
VSTM4
LOC219347
PLAC9
C10orf107
TMEM26
ZCCHC24
UNC5B
STOX1
C10orf35
TYSND1
RTKN2
C10orf27
ATOH7
SLC16A9
FAM13C
MARCH8
C10orf25
TMEM72-AS1
ZNF485
RASGEF1A
REEP3
JMJD1C
ZNF503-AS1
IPMK
FAM21C
CALHM1
SGMS1
PIPSL
PGBD3
C10orf53
BLOC1S2
FLJ37201
C10orf40
LOC283033
LOC283050
FAM149B1
FLJ31813
O3FAR1
LOC338579
DUPD1
LIPM
CYP26C1
LRIT2
LRRTM3
FAM21A
SH2D4B
C10orf99
SLC16A12
CC2D2B
LOC399753
BMS1P5
FLJ41350
GOLGA7B
MIR107
C10orf105
C10orf62
AGAP6
ZNF32-AS3
C10orf55
FAM35B
C10orf103
C10orf136
FAM35B2
LOC439990
LOC439994
IFIT1B
LOC441666
MIR346
LRRC18
MIR146B
LOC642361
AGAP9
ZNF487P
LOC642826
FAM25A
TMEM72
LIPK
LIPN
LOC643529
LOC643650
FAM25C
DRGX
LOC650623
PTPN20A
ANXA8
AGAP7
ASAH2B
SFTPA1
SNORA12
SNORD98
MIR605
MIR608
BMS1P1
ANXA8L1
FAM22A
FAM22D
LOC728190
LOC728218
AGAP8
LOC728407
LOC728558
LOC728640
LOC728643
FRMPD2P1
LOC728978
LOC729020
AGAP5
BMS1P4
SFTPA2
TLX1NB
C10orf131
LOC100128054
LOC100128292
ZNF37BP
ZNF503-AS2
FAM25B
LOC100132987
FAM25G
LOC100133308
KLLN
LOC100188947
DNMBP-AS1
TIMM23
LOC100288974
LOC100289509
MIR1287
MIR1296
MIR1256
MIR1307
FAS-AS1
MIR3157
MIR4294
MIR3158-1
MIR3156-1
MIR3158-2
MTRNR2L5
MIR3924
LOC100505540
LOC100505761
LOC100506733
LOC100506835
LOC100506939
M1
LOC100507331
LOC100507470
MARK2P9
C10orf32-AS3MT
ARHGAP19-SLIT1
MIR4679-1
MIR4679-2
MIR4676
MIR4678
MIR4685

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
ERG
TMPRSS2
hsa-mir-3197
ADARB1
AIRE
PTTG1IP
C21orf2
CBS
COL6A1
COL6A2
CRYAA
CSTB
DSCAM
DYRK1A
ETS2
HLCS
HMGN1
PRMT2
ITGB2
KCNJ6
KCNJ15
LSS
MX1
MX2
NDUFV3
PCNT
PCP4
PDE9A
PFKL
PKNOX1
PWP2
S100B
SH3BGR
SIM2
SLC19A1
SUMO3
TFF1
TFF2
TFF3
TRAPPC10
TRPM2
TTC3
U2AF1
UBE2G2
WRB
C21orf33
PDXK
RRP1
PSMG1
MCM3AP
ABCG1
DSCR4
DSCR3
B3GALT5
WDR4
FTCD
HSF2BP
RRP1B
DIP2A
POFUT2
ICOSLG
CLDN14
BACE2
C2CD2
DNMT3L
ZNF295
PIGP
UBASH3A
DSCR6
BRWD1
SLC37A1
PCBP3
C21orf58
YBEY
TSPEAR
LINC00112
LINC00111
FAM3B
RIPK4
AGPAT3
PRDM15
TMPRSS3
COL18A1
LRRC3
C21orf56
C21orf67
DSCR8
FAM207A
RSPH1
UMODL1
LINC00313
C21orf88
C21orf90
MCM3AP-AS1
LCA5L
IGSF5
SIK1
LINC00479
ZNF295-AS1
C21orf128
PLAC4
LINC00315
DSCR9
BRWD1-IT2
DSCR10
LINC00323
LINC00319
LOC284837
KRTAP12-2
KRTAP12-1
KRTAP10-10
LINC00162
COL18A1-AS1
KRTAP10-4
KRTAP10-6
KRTAP10-7
KRTAP10-9
KRTAP10-1
KRTAP10-11
KRTAP10-2
KRTAP10-5
KRTAP10-8
KRTAP10-3
KRTAP12-3
KRTAP12-4
KRTAP10-12
LINC00114
LOC642852
LINC00163
SSR4P1
LOC100129027
MIR3197
LOC100505746
DSCAM-AS1
MIR4760

Genes in Wide Peak

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

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

Genes
hsa-mir-155
hsa-mir-548x
hsa-mir-125b-2
hsa-let-7c
hsa-mir-3118-5
hsa-mir-3156-3
APP
ATP5J
BACH1
BAGE
CXADR
GABPA
NCAM2
TMPRSS15
HSPA13
TPTE
NRIP1
ADAMTS1
RWDD2B
USP16
CCT8
BTG3
ADAMTS5
LTN1
N6AMT1
USP25
RBM11
LINC00158
CHODL-AS1
LINC00113
C21orf15
LINC00308
MRPL39
C21orf91
C21orf7
JAM2
SAMSN1
BAGE5
BAGE4
BAGE3
BAGE2
MIR155HG
CYYR1
LINC00161
CHODL
ANKRD30BP2
LIPI
ABCC13
LINC00189
C21orf91-OT1
LINC00314
D21S2088E
LINC00515
POTED
LOC339622
LINC00317
LINC00320
LOC388813
LINC00478
ANKRD20A11P
MIRLET7C
MIR125B2
MIR155
MIR99A
TEKT4P2
GRIK1-AS2
MIR3156-3
MIR3687
MIR3648
C21orf37
MIR4759

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10p15.1.

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

Genes
AKR1C1
AKR1C2
AKR1C3
AKR1E2
tAKR

Genes in Wide Peak

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

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

Genes
hsa-mir-648
hsa-mir-3198
ATP6V1E1
BID
IL17RA
ANKRD62P1-PARP4P3
POTEH
BCL2L13
HSFY1P1
CECR6
CECR5
CECR3
CECR2
CECR1
MICAL3
OR11H1
SLC25A18
GAB4
CCT8L2
XKR3
TPTEP1
MIR648
CECR7
CECR5-AS1
FLJ41941
MIR3198-1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p11.1.

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

Genes
ATF1
MLL2
hsa-mir-1293
hsa-mir-1291
ACCN2
ACVR1B
ACVRL1
ADCY6
ABCD2
AMHR2
AQP2
AQP5
AQP6
ARF3
CACNB3
CCNT1
CNTN1
COL2A1
EIF4B
CELA1
GPD1
NR4A1
IGFBP6
ITGB7
KRT1
KRT2
KRT3
KRT4
KRT5
KRT6A
KRT6B
KRT7
KRT8
KRT18
KRT81
KRT82
KRT83
KRT84
KRT85
KRT86
LALBA
NELL2
SLC11A2
PCBP2
PFDN5
PFKM
POU6F1
PRKAG1
PRPH
TWF1
RARG
RNY5
SCN8A
SMARCD1
SP1
TARBP2
TMBIM6
TFCP2
VDR
WNT1
WNT10B
MAP3K12
TUBA1A
AAAS
SOAT2
ENDOU
KRT75
SCAF11
DDX23
SLC4A8
ESPL1
DAZAP2
TROAP
YAF2
TUBA1B
RAPGEF3
MCRS1
GALNT6
FAIM2
DDN
TENC1
KCNH3
ANP32D
PRPF40B
METTL7A
LETMD1
RND1
RACGAP1
SENP1
PDZRN4
DHH
PLEKHA8P1
IRAK4
FKBP11
KRT76
CSAD
BIN2
LIMA1
PPHLN1
HDAC7
SLC38A2
PRR13
KANSL2
SLC38A4
KIF21A
SLC48A1
LMBR1L
SMAGP
DIP2B
NCKAP5L
C12orf10
C12orf44
SPATS2
TMEM106C
RPAP3
DNAJC22
ADAMTS20
SLC38A1
CSRNP2
PUS7L
RACGAP1P
FAM186B
TMEM117
TUBA1C
ALG10
SPRYD3
MFSD5
C12orf62
ZCRB1
CCDC65
FMNL3
CERS5
FAM113B
KRT71
LARP4
SLC2A13
LRRK2
FAM186A
RHEBL1
C12orf54
ZNF641
OR10AD1
SP7
KRT74
ASB8
KRT72
PRICKLE1
BCDIN3D
ALG10B
CPNE8
KRT80
GRASP
KRT78
ANO6
ARID2
LOC255411
LOC283332
LOC283335
ZNF740
LOC283403
LOC283404
C12orf40
GXYLT1
TMPRSS12
KRT6C
KRT73
C1QL4
KRT79
SYT10
ANKRD33
H1FNT
OR8S1
AMIGO2
KRT77
C12orf68
LOC400027
FIGNL2
DBX2
HIGD1C
SNORA2A
SNORA2B
SNORA34
LOC100233209
LOC100286844
MIR1293
MIR1291
LOC100335030
MIR4701
MIR4698

Genes in Wide Peak

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

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

Genes
NF1
TAF15
SUZ12
hsa-mir-2909
hsa-mir-632
hsa-mir-365-2
hsa-mir-3184
hsa-mir-144
hsa-mir-1180
ACACA
ACCN1
AP2B1
ALDH3A1
ALDH3A2
ALDOC
BLMH
CPD
CRYBA1
DRG2
EVI2A
EVI2B
FOXO3B
FLII
FLOT2
KCNJ12
LGALS9
LHX1
LIG3
LLGL1
MFAP4
MYO1D
NOS2
OMG
PEX12
MAPK7
MAP2K3
PRPSAP2
PSMD11
RAD51D
RPL23A
CCL1
CCL2
CCL3
CCL3L1
CCL4
CCL5
CCL7
CCL8
CCL11
CCL13
CCL14
CCL15
CCL16
CCL18
CCL23
SDF2
SH3GL1P1
SH3GL1P2
SHMT1
SLC6A4
SUPT6H
TADA2A
HNF1B
TNFAIP1
TOP3A
VTN
RNF112
ZNF207
FOXN1
TMEM11
KSR1
CDK5R1
SLC13A2
UNC119
TIAF1
ZNHIT3
GOSR1
CCL4L1
TRAF4
KIAA0100
ULK2
FBXW10
SPAG5
CCT6B
GRAP
DDX52
DUSP14
AKAP10
SYNRG
EPN2
SARM1
USP22
PPY2
PYY2
DHRS7B
TMEM98
POLDIP2
TBC1D29
WSB1
ERAL1
AATF
SNORD4B
SNORD4A
SNORD42B
SNORD42A
B9D1
TMEM97
GIT1
SOCS7
FAM18B1
MYO15A
PIPOX
CRLF3
NLK
NLE1
FNDC8
ALKBH5
SLFN12
SLC47A1
RHOT1
C17orf79
C17orf63
ADAP2
UTP6
LYZL6
NUFIP2
TAOK1
ARHGAP23
PHF12
C17orf75
C17orf39
MMP28
DHRS11
TEFM
GGNBP2
ATAD5
MRM1
FAM106A
MYO19
SRCIN1
RAB34
NSRP1
TBC1D3F
RNF135
MRPL45
RAB11FIP4
CORO6
SSH2
TP53I13
IFT20
ZNF830
SLFN11
RASL10B
ATPAF2
SPECC1
PIGS
SLC46A1
LRRC37B
ABHD15
TLCD1
RFFL
TMEM132E
SPACA3
SGK494
SEZ6
ANKRD13B
SMCR7
SLC5A10
SMCR8
SLC47A2
C17orf50
SLFN13
SLC35G3
UNC45B
TMEM199
PROCA1
DHRS13
TRIM16L
LRRC37BP1
SLFN5
RHBDL3
C17orf108
RDM1
USP32P2
GAS2L2
TBC1D28
CDRT15L2
C17orf103
C17orf66
CCDC144B
KRT18P55
NEK8
PIGW
C17orf78
LOC284100
FAM27L
FLJ36000
LGALS9B
CCDC144NL
LOC339240
C17orf51
SLFN14
CCL14-CCL15
CCDC144C
EFCAB5
TMIGD1
CCL4L2
MYO18A
GRAPL
C17orf102
MIR144
MIR193A
TBC1D3B
TBC1D3C
CCL3L3
TBC1D3P5
SUZ12P
LOC440434
GPR179
MIR423
ARGFXP2
DPRXP4
MIR451A
FAM83G
KRT16P3
EVPLL
SEBOX
TBC1D3G
LGALS9C
SNORA59B
SNORA59A
SNORD7
MIR632
ZNF286B
TBC1D3
TBC1D3H
MIR365B
KCNJ18
C17orf96
MIR1180
MIR2909
MIR3184
MTRNR2L1
SPAG5-AS1
AA06
SLFN12L
RAD51L3-RFFL
MIR4523
MIR4724
MIR4733
MIR451B
MIR4522
MIR4732
MIR4723
MIR4725
RAB34

Genes in Wide Peak

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

Table S74. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
EGFR
ELN
HIP1
SBDS
hsa-mir-590
hsa-mir-4284
hsa-mir-4283-2
hsa-mir-3147
hsa-mir-4283-1
ASL
CACNA2D1
CCT6A
CD36
CLDN4
CLDN3
ERV3-1
GBAS
GNAI1
GTF2I
GTF2IP1
GUSB
HGF
HPVC1
HSPB1
LIMK1
MDH2
PHKG1
PMS2L2
PMS2P4
PMS2P5
PMS2P3
POR
PSPH
PTPN12
RFC2
CCL24
STX1A
EIF4H
CLIP2
LAT2
YWHAG
ZNF138
ZP3
FZD9
TPST1
FKBP6
BAZ1B
BCL7B
GTF2IRD1
MAGI2
POM121
CCL26
SEMA3C
ZNF273
FGL2
POMZP3
COBL
SEC61G
SUMF2
AUTS2
TBL2
CRCP
RABGEF1
MLXIPL
CHCHD2
ZNF117
MRPS17
ZNF107
STYXL1
PION
STAG3L1
C7orf42
TYW1
NSUN5
LANCL2
PHTF2
RHBDD2
CCDC146
WBSCR17
STAG3L4
UPK3B
VOPP1
WBSCR16
ABHD11
CALN1
TMEM120A
GTF2IRD2
DNAJC30
TMEM60
ZNF479
DTX2
WBSCR22
WBSCR28
TRIM50
SRCRB4D
VKORC1L1
KCTD7
WBSCR27
SBDSP1
VPS37D
NSUN5P1
ZNF92
ZNF679
ABHD11-AS1
VSTM2A
DKFZp434L192
SRRM3
RSBN1L
NSUN5P2
POM121L12
LOC285878
INTS4L1
LINC00174
ZNF680
SEPT14
GNAT3
ZNF713
FKBP9L
TRIM73
TRIM74
LOC389493
SPDYE8P
GATSL1
GTF2IRD2B
RPL13AP17
FLJ45974
GTF2IRD2P1
ZNF716
LOC441242
TYW1B
SPDYE7P
DTX2P1-UPK3BP1-PMS2P11
ZNF727
STAG3L3
STAG3L2
SPDYE5
LOC493754
LOC541473
FDPSL2A
LOC641746
GUSBP10
CCT6P3
CCT6P1
LOC643955
INTS4L2
LOC649395
LOC650226
NCF1
NCF1B
NCF1C
SNORA14A
SNORA15
SNORA22
MIR590
ZNF736
LOC729156
GATSL2
ZNF735
LOC100093631
POM121C
LOC100130849
LOC100132832
LOC100133091
LOC100287704
LOC100287834
MIR548M
MIR4283-2
MIR4283-1
MIR3147
MIR4284
MIR3914-1
MIR3914-2
LOC100505854
MAGI2-AS3
LOC100506050
MIR4651
MIR4650-1
MIR4650-2

Genes in Wide Peak

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

Table S75. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
IL6ST
PIK3R1
hsa-mir-583
hsa-mir-2277
hsa-mir-9-2
hsa-mir-4280
hsa-mir-582
hsa-mir-449c
hsa-mir-581
TRIM23
ARSB
BHMT
BTF3
CAST
CCNB1
CCNH
CDK7
CETN3
CHD1
CKMT2
ERCC8
COX7C
CRHBP
HAPLN1
VCAN
DHFR
F2R
F2RL1
F2RL2
FGF10
FOXD1
GHR
GLRX
GTF2H2
GZMA
GZMK
HEXB
HMGCR
HMGCS1
HTR1A
ISL1
ITGA1
ITGA2
KIF2A
TNPO1
LNPEP
CD180
MAP1B
MEF2C
MAP3K1
MOCS2
MSH3
NAIP
NDUFS4
OXCT1
PCSK1
PDE4D
PMCHL2
RAD17
RASA1
RASGRF2
RPS23
SEPP1
SMN1
SMN2
TAF9
TBCA
NR2F1
THBS4
XRCC4
ZNF131
SERF1A
ENC1
AP3B1
PPAP2A
PDE8B
HSPB3
HOMER1
SCAMP1
CARTPT
TTC37
ZFYVE16
EDIL3
COL4A3BP
LHFPL2
CWC27
CCNO
NSA2
FST
PAIP1
POLR3G
PLK2
IQGAP2
MRPS30
SMA4
SMA5
ESM1
ADAMTS6
RHOBTB3
ELL2
SV2C
MRPS27
PPWD1
OTP
SKIV2L2
NNT
SSBP2
BHMT2
PART1
FAM169A
FBXO4
RNU5E-1
RNU5D-1
DIMT1
DMGDH
IPO11
GCNT4
POLK
ERAP1
PELO
DHX29
DDX4
SGTB
ARL15
AGGF1
WDR41
RIOK2
DEPDC1B
BDP1
ERBB2IP
CCL28
NLN
ARRDC3
ZSWIM6
ANKRA2
MCCC2
CENPK
ERAP2
RGNEF
C5orf28
SLC30A5
CENPH
GPBP1
PARP8
ANKRD55
MCTP1
PTCD2
ELOVL7
C5orf44
ATG10
SPATA9
FAM172A
GPR98
UTP15
ZCCHC9
ANKRD32
ZBED3
GFM2
SPZ1
NDUFAF2
MRPS36
ATP6AP1L
SNX18
FCHO2
RAB3C
LYSMD3
C5orf35
IL31RA
EMB
JMY
POU5F2
TMEM171
TMEM174
POC5
ACOT12
SREK1
SLC38A9
TMEM167A
MBLAC2
TMEM161B
MARVELD2
ARSK
FAM81B
LOC153684
MIER3
CDC20B
PAPD4
NIM1
LIX1
ZNF366
FAM151B
S100Z
CCDC125
C5orf27
GAPT
CMYA5
ANKRD31
SERINC5
LOC257396
KIAA0825
GPR150
NBPF22P
C5orf51
C5orf64
RNF180
SREK1IP1
RGMB
RFESD
ANKRD34B
IDAS
ACTBL2
MTX3
HCN1
C5orf34
MAST4
RNF138P1
C5orf39
RGS7BP
MIR9-2
CRSP8P
FLJ42709
GPX8
FLJ35946
MIR449A
LOC642366
C5orf43
LOC644936
LINC00461
LOC647859
LOC648987
GUSBP3
GTF2H2B
SCARNA18
SNORA47
MIR449B
MIR581
MIR583
GTF2H2C
SERF1B
LOC728723
GTF2H2D
GUSBP9
LOC100129716
CCDC152
LRRC70
LOC100131067
LOC100132356
FAM159B
LOC100170939
LOC100272216
LOC100289230
NCRUPAR
LOC100303749
MIR2277
MIR449C
MIR4280
MTRNR2L2
MIR3607
MIR3660
LOC100505894
OCLN
MIR4804
MIR3977
MIR4803

Arm-level results

Table 3. Get Full Table Arm-level significance table - 23 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.06 | 0.499 | 0.802 | 0.09 | 2.78 | 0.0097
1q | 1955 | 0.14 | 5.47 | 2.91e-07 | 0.03 | -2.01 | 1
2p | 924 | 0.09 | -1.51 | 1 | 0.02 | -4.89 | 1
2q | 1556 | 0.06 | -1.7 | 1 | 0.03 | -3.1 | 1
3p | 1062 | 0.11 | -0.275 | 1 | 0.54 | 22.1 | 0
3q | 1139 | 0.45 | 17.4 | 0 | 0.22 | 4.57 | 1.2e-05
4p | 489 | 0.06 | -3.57 | 1 | 0.26 | 5.43 | 1.54e-07
4q | 1049 | 0.03 | -4.19 | 1 | 0.16 | 2.41 | 0.0242
5p | 270 | 0.28 | 5.4 | 3.31e-07 | 0.17 | 0.485 | 0.612
5q | 1427 | 0.10 | 0.209 | 0.904 | 0.27 | 9.93 | 0
6p | 1173 | 0.09 | -0.989 | 1 | 0.11 | -0.0941 | 0.953
6q | 839 | 0.05 | -3.69 | 1 | 0.11 | -1.04 | 1
7p | 641 | 0.22 | 3.85 | 0.000284 | 0.05 | -3.72 | 1
7q | 1277 | 0.15 | 2.46 | 0.021 | 0.09 | -0.481 | 1
8p | 580 | 0.24 | 3.97 | 0.000203 | 0.40 | 11.6 | 0
8q | 859 | 0.46 | 16.3 | 0 | 0.14 | 0.489 | 0.612
9p | 422 | 0.21 | 2.54 | 0.0178 | 0.36 | 9 | 0
9q | 1113 | 0.20 | 4.29 | 7e-05 | 0.16 | 2.37 | 0.0247
10p | 409 | 0.05 | -4.21 | 1 | 0.17 | 0.772 | 0.497
10q | 1268 | 0.02 | -4.4 | 1 | 0.10 | 0.0217 | 0.912
11p | 862 | 0.07 | -2.42 | 1 | 0.20 | 3.7 | 0.000429
11q | 1515 | 0.10 | 0.386 | 0.802 | 0.29 | 11.9 | 0
12p | 575 | 0.22 | 3.73 | 0.000421 | 0.07 | -3.27 | 1
12q | 1447 | 0.10 | 0.396 | 0.802 | 0.06 | -1.93 | 1
13q | 654 | 0.09 | -2.13 | 1 | 0.23 | 4.33 | 3.26e-05
14q | 1341 | 0.17 | 4.15 | 0.000107 | 0.07 | -1.65 | 1
15q | 1355 | 0.04 | -3.03 | 1 | 0.09 | -0.388 | 1
16p | 872 | 0.06 | -3.04 | 1 | 0.07 | -2.71 | 1
16q | 702 | 0.08 | -2.42 | 1 | 0.09 | -2.1 | 1
17p | 683 | 0.07 | -2.82 | 1 | 0.16 | 1.16 | 0.32
17q | 1592 | 0.08 | -0.0985 | 1 | 0.03 | -3.15 | 1
18p | 143 | 0.19 | 1.2 | 0.323 | 0.19 | 1.05 | 0.356
18q | 446 | 0.08 | -2.75 | 1 | 0.32 | 7.95 | 6.49e-15
19p | 995 | 0.04 | -3.72 | 1 | 0.11 | -0.289 | 1
19q | 1709 | 0.07 | -0.316 | 1 | 0.09 | 0.741 | 0.497
20p | 355 | 0.21 | 2.59 | 0.0172 | 0.07 | -3.37 | 1
20q | 753 | 0.20 | 3.41 | 0.00127 | 0.06 | -3.21 | 1
21q | 509 | 0.03 | -4.8 | 1 | 0.20 | 2.45 | 0.0235
22q | 921 | 0.12 | -0.0237 | 1 | 0.09 | -1.37 | 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.

- 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/1444432/2.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 = 0.30

- Deletion Threshold = 0.30

- Cap Values = 2.0

- Broad Length Cutoff = 0.5

- Remove X-Chromosome = 1

- Confidence Level = 0.99

- Join Segment Size = 10

- Arm Level Peel Off = 1

- Maximum Sample Segments = 10000

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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