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

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. The pipeline first filters out normal samples from the segmented copy-number data by inspecting the TCGA barcodes and then executes GISTIC version 2.0.16 (cga svn revision 38839).

Summary

There were 282 tumor samples used in this analysis: 28 significant arm-level results, 31 significant focal amplifications, and 42 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 - 31 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband | Q value | Residual Q value | Wide Peak Boundaries | # Genes in Wide Peak
--- | --- | --- | --- | ---
3q26.33 | 1.6842e-75 | 1.6842e-75 | chr3:182587252-182650693 | 1
8p11.23 | 3.8994e-48 | 3.8994e-48 | chr8:38170522-38251736 | 2
11q13.3 | 2.1632e-44 | 2.1632e-44 | chr11:69699947-69910839 | 0 [ANO1]
7p11.2 | 6.1178e-18 | 7.0856e-18 | chr7:54781785-55440774 | 3
8q24.21 | 1.0694e-14 | 1.0694e-14 | chr8:128359656-128478159 | 2
2p16.1 | 6.6256e-12 | 6.6256e-12 | chr2:60529126-60940831 | 2
4q12 | 1.0541e-10 | 1.0541e-10 | chr4:56251657-56507740 | 5
18q11.2 | 2.9049e-06 | 2.9049e-06 | chr18:23753292-24009885 | 2
9p13.3 | 2.2662e-06 | 8.8373e-06 | chr9:34812718-35059852 | 5
20q11.21 | 5.8018e-05 | 5.8018e-05 | chr20:26196264-30629902 | 27
19q13.2 | 2.2344e-09 | 6.7076e-05 | chr19:39592139-40066564 | 22
1q21.2 | 8.5791e-05 | 8.5791e-05 | chr1:120523956-152366921 | 158
14q13.3 | 0.0002781 | 0.0002781 | chr14:36782985-38160246 | 10
19q12 | 3.2444e-05 | 0.00074785 | chr19:28697976-30768475 | 10
1p34.2 | 0.00098645 | 0.00098645 | chr1:39753329-40650788 | 18
2q31.2 | 0.0006252 | 0.0010136 | chr2:178078954-178131695 | 4
7q21.2 | 0.0012547 | 0.0013829 | chr7:92196092-93139812 | 11
5p15.33 | 0.0025602 | 0.0025602 | chr5:1-2409177 | 34
12q15 | 0.0069212 | 0.0069212 | chr12:66887415-71869014 | 32
15q26.3 | 0.01217 | 0.01217 | chr15:91937097-102531392 | 53
6q22.31 | 0.009736 | 0.012746 | chr6:124723543-125774018 | 5
6q12 | 0.019926 | 0.025635 | chr6:63667925-66482646 | 4
17q25.1 | 0.0093413 | 0.032791 | chr17:70568509-74574131 | 102
3p11.1 | 0.035553 | 0.035553 | chr3:89150943-90283073 | 1
17q23.1 | 0.01315 | 0.055927 | chr17:57918371-57946458 | 3
9p24.1 | 0.043212 | 0.056974 | chr9:5421313-5592144 | 3
12p13.33 | 0.094302 | 0.094302 | chr12:1-3615076 | 35
11p15.2 | 0.11333 | 0.11333 | chr11:14258656-14797944 | 5
18p11.32 | 0.17547 | 0.17547 | chr18:1-4877663 | 27
21q21.1 | 0.19712 | 0.19712 | chr21:1-20885987 | 39
2q11.2 | 0.16389 | 0.2456 | chr2:95885683-99809139 | 51

Genes in Wide Peak

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

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

Genes
ATP11B

Genes in Wide Peak

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

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

Genes
WHSC1L1
LETM2

Genes in Wide Peak

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

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

Genes
EGFR
SEC61G
LANCL2

Genes in Wide Peak

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

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

Genes
POU5F1B
LOC727677

Genes in Wide Peak

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

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

Genes
BCL11A
MIR4432

Genes in Wide Peak

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

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

Genes
CLOCK
NMU
TMEM165
PDCL2
LOC100506462

Genes in Wide Peak

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

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

Genes
TAF4B
PSMA8

Genes in Wide Peak

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

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

Genes
VCP
KIAA1045
DNAJB5
C9orf131
FAM205B

Genes in Wide Peak

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

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

Genes
hsa-mir-3193
BCL2L1
FOXS1
ID1
TPX2
REM1
HM13
PDRG1
COX4I2
MYLK2
DEFB118
DUSP15
MLLT10P1
C20orf160
LINC00028
TTLL9
DEFB115
DEFB116
DEFB119
DEFB121
DEFB122
DEFB123
DEFB124
FRG1B
XKR7
PSIMCT-1
MIR3193

Genes in Wide Peak

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

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

Genes
RPS16
SUPT5H
ZFP36
GMFG
PAK4
DLL3
PAF1
SAMD4B
MED29
LRFN1
PLEKHG2
TIMM50
EID2B
EID2
IL28A
IL28B
IL29
NCCRP1
SYCN
SELV
PAPL
MIR4530

Genes in Wide Peak

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

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

Genes
ARNT
BCL9
NOTCH2
PDE4DIP
hsa-mir-554
hsa-mir-4257
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
CTSK
CTSS
ECM1
ENSA
FCGR1A
FCGR1B
FLG
FMO5
GJA5
GJA8
MCL1
PDZK1
PI4KB
PRKAB2
PSMB4
PSMD4
RFX5
RORC
S100A10
S100A11
VPS72
TCHH
TUFT1
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
PIP5K1A
ANXA9
ITGA10
PEX11B
SELENBP1
PRPF3
SEC22B
CHD1L
SETDB1
SV2A
RBM8A
SF3B4
PIAS3
SEMA6C
POLR3C
TXNIP
MTMR11
MLLT11
TDRKH
CD160
CELF3
VPS45
POGZ
RPRD2
CA14
NBPF14
RNF115
TMOD4
CERS2
BOLA1
APH1A
PLEKHO1
ACP6
GPR89B
OAZ3
MRPS21
ADAMTSL4
C1orf56
GOLPH3L
FAM63A
CDC42SE1
OTUD7B
FAM91A2
CGN
ZNF687
PRUNE
MRPL9
SCNM1
TNFAIP8L2
C1orf54
TARS2
SNX27
ANP32E
HORMAD1
POLR3GL
GNRHR2
THEM4
GABPB2
TCHHL1
RPTN
HIST2H3C
LIX1L
C1orf51
HFE2
ANKRD35
BNIPL
PPIAL4A
PDIA3P
NBPF11
NUDT17
RIIAD1
THEM5
NBPF15
ANKRD34A
HIST2H2AB
HIST2H3A
HIST2H2BC
HIST2H2BA
LINGO4
LOC375010
NOTCH2NL
FLJ39739
LOC388692
LYSMD1
HRNR
FLG2
NBPF9
HIST2H2BF
HIST2H4B
PPIAL4G
PPIAL4D
LOC645166
EMBP1
SRGAP2P2
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
MIR554
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
LOC100130000
LOC100132111
NBPF10
FCGR1C
C2CD4D
LOC100286793
LOC100289211
MIR4257
TNFAIP8L2-SCNM1

Genes in Wide Peak

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

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

Genes
NKX2-1
FOXA1
PAX9
NKX2-8
MBIP
SLC25A21
MIPOL1
SFTA3
LOC100129794
MIR4503

Genes in Wide Peak

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

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

Genes
CCNE1
UQCRFS1
URI1
POP4
PLEKHF1
C19orf12
LOC148145
LOC284395
VSTM2B
LOC100505835

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p34.2.

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

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

Genes in Wide Peak

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

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

Genes
NFE2L2
hsa-mir-3128
HNRNPA3
MIR3128

Genes in Wide Peak

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

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

Genes
CDK6
hsa-mir-489
CALCR
SAMD9
CCDC132
SAMD9L
HEPACAM2
FAM133B
MIR489
MIR653
LOC728066

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
MDM2
hsa-mir-1279
CPM
IFNG
LYZ
CNOT2
PTPRB
PTPRR
RAP1B
TSPAN8
YEATS4
DYRK2
LGR5
CCT2
FRS2
CPSF6
GRIP1
KCNMB4
IL22
SLC35E3
IL26
CAND1
MDM1
NUP107
RAB3IP
BEST3
LRRC10
MIR1279
SNORA70G
MIR3913-2
MIR3913-1
LOC100507250

Genes in Wide Peak

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

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

Genes
hsa-mir-1302-10
hsa-mir-1469
hsa-mir-3175
ALDH1A3
CHD2
IGF1R
MEF2A
PCSK6
SNRPA1
NR2F2
ST8SIA2
CHSY1
SYNM
OR4F4
SLCO3A1
LINS
MCTP2
SELS
RGMA
TTC23
LRRK1
TM2D3
ARRDC4
LOC91948
TARSL2
LRRC28
ASB7
LYSMD4
PGPEP1L
LOC145820
C15orf32
SPATA8
ADAMTS17
DNM1P46
CERS3
FAM169B
WASH3P
FLJ42289
OR4F6
OR4F15
FAM174B
LOC400456
ASB9P1
FAM138E
LOC100144604
GPCRLTM7
DDX11L1
DDX11L9
MIR1469
MIR3175
LOC100507217
LOC100507472
MIR4714

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q22.31.

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

Genes
STL
TPD52L1
HDDC2
RNF217
NKAIN2

Genes in Wide Peak

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

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

Genes
PTP4A1
PHF3
LGSN
EYS

Genes in Wide Peak

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

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

Genes
AANAT
ACOX1
CDK3
EVPL
FDXR
FOXJ1
GALK1
GRB2
GRIN2C
H3F3B
ICT1
ITGB4
LLGL2
PRPSAP1
RPL38
SUMO2
SRP68
SSTR2
GALR2
SPHK1
SLC16A5
SLC9A3R1
COG1
RECQL5
KIAA0195
ATP5H
ST6GALNAC2
CD300C
CD300A
GGA3
EXOC7
KCTD2
WBP2
CDC42EP4
NAT9
SAP30BP
NT5C
CDR2L
MRPS7
HN1
SDK2
TMEM104
C17orf80
GPRC5C
MIF4GD
CASKIN2
SLC25A19
UBE2O
DNAI2
MRPL38
ARMC7
RHBDF2
NUP85
MYO15B
QRICH2
FAM104A
MGC16275
FBF1
UNK
TRIM47
OTOP2
TTYH2
CYGB
RNF157
USH1G
CD300LB
KIF19
CD300LF
C17orf77
SLC39A11
TRIM65
UNC13D
LINC00469
FADS6
C17orf28
TSEN54
FAM100B
RAB37
CD300E
OTOP3
GPR142
ZACN
BTBD17
LINC00511
LOC400620
CPSF4L
C17orf109
SNORD1A
SNORD1B
SNORD1C
PRCD
C17orf110
CD300LD
TEN1
LOC100287042
LOC100499467
MIR3678
MIR3615
LOC100507218
LOC100507246
TEN1-CDK3
MIR4738

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3p11.1.

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

Genes
EPHA3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 17q23.1.

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

Genes
hsa-mir-21
TUBD1
MIR21

Genes in Wide Peak

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

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

Genes
CD274
C9orf46
PDCD1LG2

Genes in Wide Peak

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

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

Genes
KDM5A
CACNA1C
FKBP4
FOXM1
NINJ2
RAD52
SLC6A12
SLC6A13
TEAD4
TULP3
TSPAN9
ERC1
ITFG2
PRMT8
WNK1
ADIPOR2
WNT5B
C12orf32
NRIP2
CCDC77
CACNA2D4
FBXL14
DCP1B
B4GALNT3
LOC283440
IQSEC3
LOC574538
LRTM2
FAM138D
LOC100271702
LOC100288778
LOC100292680
MIR3649
LOC100507424
LOC100652846

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p15.2.

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

Genes
COPB1
PDE3B
PSMA1
SPON1
RRAS2

Genes in Wide Peak

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

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

Genes
ADCYAP1
CETN1
TGIF1
TYMS
YES1
MYOM1
USP14
DLGAP1
LPIN2
THOC1
NDC80
MYL12A
SMCHD1
CLUL1
ENOSF1
LINC00470
METTL4
COLEC12
EMILIN2
MYL12B
LOC201477
LOC284215
C18orf56
CBX3P2
FLJ35776
ROCK1P1
LOC727896

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
hsa-mir-3127
ADRA2B
CNGA3
COX5B
DUSP2
INPP4A
ZAP70
CIAO1
ACTR1B
ARID5A
MGAT4A
SNRNP200
NCAPH
TMEM131
UNC50
CNNM4
CNNM3
KCNIP3
FAHD2A
ANKRD39
FAM178B
MRPL30
LIPT1
SEMA4C
TMEM127
KANSL3
STARD7
ANKRD36B
TSGA10
LMAN2L
FER1L5
NEURL3
MITD1
TRIM43
C2orf15
PROM2
GPAT2
ITPRIPL1
FAHD2B
VWA3B
ANKRD23
LOC285033
C2orf55
ANKRD36
ASTL
COA5
TRIM43B
LOC728537
LOC729234
MIR3127
LOC100506123

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 - 42 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 | 1.9284e-92 | 1.9666e-85 | chr9:21865498-21996995 | 2
8p23.2 | 1.656e-39 | 1.656e-39 | chr8:2079140-6262191 | 1
2q22.1 | 8.6257e-30 | 2.0236e-25 | chr2:139655617-143637838 | 1
10q23.31 | 8.963e-15 | 8.963e-15 | chr10:89617158-90034038 | 2
5q11.2 | 1.4965e-13 | 4.6805e-13 | chr5:58260298-59787985 | 3
4q35.2 | 1.6059e-10 | 8.7144e-08 | chr4:187205302-188227950 | 3
3p25.3 | 1.1538e-07 | 1.4271e-07 | chr3:11593528-11833472 | 1
2q37.3 | 7.3328e-12 | 1.7633e-07 | chr2:210440283-243199373 | 297
11p15.5 | 7.0332e-07 | 7.1763e-07 | chr11:1-4907071 | 139
4q22.1 | 1.7633e-07 | 3.7836e-06 | chr4:90844993-93240505 | 1
3p11.1 | 3.7012e-11 | 4.6377e-06 | chr3:89525001-93777876 | 3
11q25 | 6.4686e-05 | 6.5841e-05 | chr11:126870419-135006516 | 36
1p13.1 | 2.9537e-05 | 8.1411e-05 | chr1:108022648-149898950 | 235
9p13.1 | 1.9145e-07 | 8.1411e-05 | chr9:38619152-71152237 | 50
13q14.2 | 1.8637e-06 | 0.00010653 | chr13:48833767-49003156 | 1
3p12.3 | 1.0398e-12 | 0.00022409 | chr3:77699023-84688247 | 2
3p13 | 2.4499e-11 | 0.00032536 | chr3:70016017-71729299 | 3
21q21.1 | 0.00038472 | 0.00040203 | chr21:1-22117102 | 39
19p13.3 | 0.00064286 | 0.00067326 | chr19:1-1386003 | 56
7q11.22 | 0.0017842 | 0.0026545 | chr7:66780207-70601215 | 1
15q13.3 | 0.0035197 | 0.0035488 | chr15:1-44170698 | 312
9p21.2 | 2.6824e-15 | 0.0037684 | chr9:27572512-28982153 | 4
17q11.2 | 0.0019054 | 0.0040956 | chr17:29326736-29651479 | 5
13q12.11 | 0.00022402 | 0.0053892 | chr13:1-23755126 | 28
18q23 | 0.0063985 | 0.0063985 | chr18:73139336-78077248 | 19
22q11.21 | 0.0065086 | 0.0063985 | chr22:1-22114035 | 116
17q25.3 | 0.0063985 | 0.010017 | chr17:80031841-81195210 | 22
19q13.33 | 0.011643 | 0.011583 | chr19:46233298-59128983 | 574
6q26 | 0.013915 | 0.014227 | chr6:146758670-171115067 | 144
10p15.3 | 0.01511 | 0.015548 | chr10:1-1040137 | 5
16p13.3 | 0.016278 | 0.016369 | chr16:1-6071497 | 227
4q32.2 | 0.00019829 | 0.018992 | chr4:164439857-165912961 | 6
16q12.1 | 0.041224 | 0.043214 | chr16:50714030-51170345 | 3
7q36.1 | 0.027537 | 0.043767 | chr7:117882615-159138663 | 336
16q23.1 | 0.043767 | 0.043767 | chr16:73455019-90354753 | 153
1p36.12 | 0.0013426 | 0.075217 | chr1:1-32940451 | 532
9p24.1 | 0.0022944 | 0.079962 | chr9:7799607-13928229 | 5
4p15.31 | 0.088805 | 0.088169 | chr4:20726855-22330985 | 2
14q11.2 | 0.095901 | 0.095976 | chr14:1-50045002 | 235
5q15 | 0.025734 | 0.11621 | chr5:61683961-180915260 | 808
1p36.23 | 0.0020486 | 0.15416 | chr1:1-32940451 | 532
12q24.33 | 0.15985 | 0.16337 | chr12:82751484-133851895 | 409

Genes in Wide Peak

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

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

Genes
CSMD1

Genes in Wide Peak

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

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

Genes
LRP1B

Genes in Wide Peak

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

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

Genes
PTEN
KLLN

Genes in Wide Peak

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

Table S35. 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 4q35.2.

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

Genes
FAT1
MTNR1A
LOC285441

Genes in Wide Peak

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

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

Genes
VGLL4

Genes in Wide Peak

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

Table S38. 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
hsa-mir-548f-2
AAMP
ACADL
AGXT
ALPI
ALPP
ALPPL2
KIF1A
BARD1
BCS1L
BOK
CHRND
CHRNG
COL4A3
COL4A4
COL6A3
CPS1
CRYBA2
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
PTMA
PTPRN
SNORD20
RPE
RPL37A
SAG
CCL20
SLC4A3
SLC11A1
SP100
SPP2
TNP1
TNS1
TUBA4A
VIL1
WNT6
XRCC5
ZNF142
SCG2
CUL3
DGKD
STK16
PER2
CDK5R2
RQCD1
LRRFIP1
GPR55
TRIP12
ECEL1
EIF4E2
TTLL4
HDAC4
FARP2
FARSB
ABCB6
ARPC2
ARL4C
RAMP1
SPEG
LANCL1
NMUR1
STK25
COPS8
CAPN10
SP140
IKZF2
PASK
ATG4B
OBSL1
DNPEP
SH3BP4
KCNE4
NGEF
SNORD82
PNKD
SNED1
GIGYF2
TRAF3IP1
ABCA12
CNPPD1
STK36
CPS1-IT1
GMPPA
SMARCAL1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
CAB39
PRKAG3
UGT1A10
UGT1A8
UGT1A7
UGT1A6
UGT1A5
UGT1A9
UGT1A4
UGT1A1
UGT1A3
PID1
ATG16L1
ANKZF1
USP40
HJURP
HES6
ACCN4
DOCK10
MREG
PECR
C2orf83
MFF
CXCR7
RNPEPL1
MARCH4
WDFY1
NYAP2
USP37
CTDSP1
GAL3ST2
TMBIM1
RAB17
RNF25
COPS7B
MRPL44
TRPM8
ATG9A
MLPH
FAM134A
GLB1L
SPAG16
CHPF
IQCA1
NHEJ1
FAM124B
TM4SF20
C2orf54
TUBA4B
ARMC9
EFHD1
SPHKAP
WNT10A
SLC19A3
ILKAP
ITM2C
RHBDD1
ING5
PLCD4
MGC16025
TMEM169
DNER
B3GNT7
SP140L
STK11IP
MOGAT1
AGAP1
TWIST2
DIS3L2
NEU4
AP1S3
SGPP2
SPATA3
TMEM198
ZFAND2B
FBXO36
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
LOC150935
PKI55
C2orf67
LOC151171
LOC151174
CCDC140
SLC23A3
LOC151300
GPBAR1
SLC16A14
LOC151475
LINC00471
LOC151484
MSL3P1
WDR69
C2orf57
TIGD1
LOC200772
CCDC108
C2orf72
CXXC11
UNC80
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
MIR548F2
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 11p15.5.

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

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

Genes in Wide Peak

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

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

Genes
FAM190A

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p11.1.

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

Genes
PROS1
ARL13B
STX19

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
BCL9
NOTCH2
NRAS
PDE4DIP
TRIM33
RBM15
hsa-mir-3118-3
hsa-mir-3118-2
hsa-mir-3118-1
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
ADORA3
ALX3
AMPD1
AMPD2
RHOC
ATP1A1
ATP5F1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CSF1
CELSR2
FCGR1A
FCGR1B
FMO5
GJA5
GJA8
GNAI3
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
HMGCS2
HSD3B1
HSD3B2
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PDZK1
PRKAB2
PSMA5
PTGFRN
RAP1A
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TSHB
WNT2B
CSDE1
HIST2H2AA3
HIST2H2AC
HIST2H2BE
HIST2H4A
TTF2
ITGA10
PEX11B
SLC16A4
CD101
SEC22B
CHD1L
LRIG2
SV2A
RBM8A
TSPAN2
BCAS2
WARS2
CEPT1
PIAS3
VAV3
HBXIP
POLR3C
TXNIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
ADAM30
CD160
DDX20
WDR47
CLCC1
NBPF14
PTPN22
PHGDH
CHIA
RNF115
GPSM2
SLC25A24
BOLA1
HAO2
ACP6
GPR89B
RSBN1
GDAP2
FAM46C
ST7L
PRPF38B
SLC22A15
LRIF1
CTTNBP2NL
FAM212B
TMEM167B
OLFML3
FAM91A2
AMIGO1
KIAA1324
DCLRE1B
WDR77
EPS8L3
VTCN1
DENND2D
SIKE1
TRIM45
VANGL1
GPR61
REG4
POLR3GL
PROK1
PSRC1
ATP1A1OS
FAM40A
ZNF697
HENMT1
GNRHR2
MAB21L3
HIST2H3C
ATXN7L2
C1orf194
LIX1L
HSD3BP4
DRAM2
C1orf88
C1orf162
SYT6
NBPF4
HFE2
ANKRD35
RP11-165H20.1
DENND2C
FNDC7
PPIAL4A
UBL4B
PDIA3P
NBPF11
NUDT17
SPAG17
HIPK1
AKR7A2P1
AKNAD1
MAGI3
FAM19A3
NBPF15
FAM102B
SYPL2
CYB561D1
ANKRD34A
HIST2H2AB
PPM1J
HIST2H3A
HIST2H2BC
HIST2H2BA
MYBPHL
NBPF7
LOC375010
SLC6A17
NOTCH2NL
FLJ39739
LOC388692
NBPF9
MIR197
LOC440600
BCL2L15
HIST2H2BF
PGCP1
HIST2H4B
SRG7
CYMP
LOC643441
LOC644242
PPIAL4G
PPIAL4D
LOC645166
EMBP1
SRGAP2P2
NBPF6
PPIAL4B
LOC653513
GPR89A
PPIAL4C
HIST2H3D
FAM72B
SCARNA2
HIST2H2AA4
FAM72D
LOC728855
LOC728875
NBPF24
GPR89C
NBPF16
PDZK1P1
PPIAL4F
LOC728989
PPIAL4E
PFN1P2
MIR942
LOC100129269
LOC100130000
NBPF10
FCGR1C
LOC100286793
LOC100287722
LOC100289211
MIR320B1
MIR4256
LOC100506343

Genes in Wide Peak

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

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

Genes
LPAR6

Genes in Wide Peak

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

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

Genes
GBE1
ROBO1

Genes in Wide Peak

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

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

Genes
FOXP1
hsa-mir-1284
MIR1284

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
AUTS2

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q13.3.

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

Genes
BUB1B
C15orf55
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
NBEAP1
CAPN3
CHRM5
CHRNA7
CKMT1B
EPB42
GABRA5
GABRB3
GABRG3
GANC
GCHFR
PDIA3
IPW
ITPKA
IVD
LTK
MAP1A
MEIS2
MFAP1
TRPM1
NDN
OCA2
PLCB2
RAD51
RYR3
SCG5
SNRPN
SPINT1
SRP14
THBS1
TJP1
TP53BP1
TYRO3
UBE3A
MKRN3
PAR5
JMJD7-PLA2G4B
SNAP23
HERC2
SNURF
TGM5
PPIP5K1
AQR
ARHGAP11A
LCMT2
SLC12A6
RASGRP1
SERF2
GPR176
CHP
OIP5
BAHD1
FAN1
MAPKBP1
GOLGA8A
RTF1
CYFIP1
MGA
VPS39
FAM189A1
CCNDBP1
C15orf2
C15orf63
TMEM87A
RPAP1
DKFZP434L187
GREM1
RPUSD2
TUBGCP4
EHD4
NDUFAF1
NUSAP1
TMEM85
SPTBN5
KLF13
MAGEL2
DLL4
INO80
PPP1R14D
MTMR10
ZNF770
HAUS2
FAM82A2
DNAJC17
NOP10
NDNL2
C15orf24
PAK6
CASC5
AVEN
ATP10A
GJD2
STARD9
VPS18
ZFP106
CHAC1
C15orf29
WDR76
TMEM62
ELL3
NIPA2
C15orf41
ZFYVE19
DISP2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
ATPBD4
C15orf57
C15orf23
BMF
SNORD107
CHST14
TUBGCP5
TGM7
CATSPER2
NIPA1
PLA2G4E
PAR1
LOC145845
TMCO5A
ZSCAN29
TTBK2
CDAN1
STRC
CSNK1A1P1
OTUD7A
SPRED1
PGBD4
ADAL
EXD1
FSIP1
RHOV
UBR1
LPCAT4
PLA2G4F
LRRC57
LOC283683
OR4N4
LOC283710
FAM98B
PLA2G4D
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
FMN1
SNORD64
PAR4
PAR-SN
LOC348120
MRPL42P5
C15orf52
GOLGA8E
OR4M2
OR4N3P
HERC2P2
C15orf53
C15orf54
MIR211
NF1P2
HERC2P9
WHAMMP2
GOLGA8B
EIF2AK4
CATSPER2P1
LOC503519
CKMT1A
SERINC4
C15orf62
C15orf56
PHGR1
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
LOC100128714
LOC100131089
ANKRD63
HERC2P7
GOLGA8F
GOLGA8DP
JMJD7
PLA2G4B
ULK4P2
LOC100288615
LOC100288637
LOC100289656
MIR1233-1
MIR1282
MIR1233-2
MIR4310
MIR3942
LOC100505648
LOC100507466
SERF2-C15ORF63
MIR4509-1
MIR4509-2
MIR4508
MIR4510
MIR4509-3
MIR4715
TMCO5B

Genes in Wide Peak

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

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

Genes
hsa-mir-873
LINGO2
MIR876
MIR873

Genes in Wide Peak

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

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

Genes
NF1
EVI2A
EVI2B
OMG
MIR4733

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
KLK2
PPP2R1A
TFPT
ZNF331
hsa-mir-1274b
hsa-mir-935
hsa-mir-373
hsa-mir-1283-2
hsa-mir-643
hsa-mir-125a
hsa-mir-150
hsa-mir-4324
hsa-mir-220c
hsa-mir-3191
hsa-mir-320e
hsa-mir-769
A1BG
AP2A1
KLK3
BAX
BCAT2
C5AR1
CA11
CALM3
CD33
SIGLEC6
CD37
CGB
AP2S1
CRX
DBP
DMPK
DMWD
EMP3
ETFB
FCAR
FCGRT
FKBP1AP1
FLT3LG
FPR1
FPR2
FPR3
FTL
FUT1
FUT2
GPR32
GRIN2D
ARHGAP35
GYS1
HAS1
FOXA3
HRC
PRMT1
IL11
IRF3
KCNA7
KCNC3
KCNJ14
KIR2DL1
KIR2DL3
KIR2DL4
KIR2DS4
KIR3DL1
KIR3DL2
KLK1
LAIR1
LAIR2
LHB
LIG1
LIM2
MYBPC2
NDUFA3
NKG7
CNOT3
NOVA2
NPAS1
NTF4
NUCB1
PEG3
POLD1
PPP5C
PRKCG
PRRG2
KLK7
KLK6
KLK10
PTGIR
PTPRH
RPL18
RPL28
RPS5
RPS9
RPS11
RRAS
CLEC11A
SEPW1
SLC1A5
SLC8A2
SNRNP70
SPIB
AURKC
SULT2B1
SULT2A1
SYT5
TNNI3
TNNT1
TULP2
NR1H2
ZNF8
ZNF17
ZNF28
MZF1
ZNF132
ZNF134
ZNF135
ZNF137P
ZNF154
ZNF175
SYMPK
TEAD2
PPFIA3
PLA2G4C
NAPA
SIGLEC5
PGLYRP1
UBE2M
CYTH2
ZNF264
NCR1
NAPSA
KLK4
ZNF432
DHX34
SAE1
TRIM28
ZNF256
LILRB2
ZNF211
TRAPPC2P1
ZNF274
ZNF460
RUVBL2
LILRB1
KDELR1
LILRB5
SLC27A5
LILRB4
KLK11
LILRA1
LILRB3
LILRA3
LILRA2
KPTN
KLK8
PNKP
U2AF2
ATF5
PPP6R1
CARD8
ZC3H4
RPL13A
SYNGR4
LILRA4
ZIM2
NUP62
HSPBP1
PPP1R15A
ZNF324
KLK5
PRKD2
ZNF473
KLK13
CCDC9
PRPF31
IRF2BP1
FGF21
SNORD35A
SNORD34
SNORD33
SNORD32A
SIGLEC7
BBC3
DKKL1
SIGLEC9
SIGLEC8
GPR77
CHMP2A
DHDH
ZNF544
UBE2S
SLC6A16
STRN4
CCDC106
EPN1
GLTSCR2
GLTSCR1
EHD2
KLK14
KLK12
SHANK1
NOSIP
ZNF580
HSD17B14
GP6
VRK3
ZNF581
PTOV1
PPP1R12C
TRPM4
ZNF586
FAM83E
EPS8L1
RASIP1
TMEM160
PIH1D1
C19orf73
PNMAL1
TMEM143
ZNF444
KLK15
NLRP2
ZNF416
ZNF446
ZNF701
ZNF83
ZNF415
CABP5
SPHK2
MEIS3
SLC17A7
NAT14
VN1R1
RCN3
ZNF304
TTYH1
PNMAL2
PRR12
ZNF471
USP29
PLEKHA4
ZNF71
SCAF1
CACNG8
CACNG7
CACNG6
ZNF350
TSKS
ZNF667
ELSPBP1
LIN7B
HIF3A
ZNF649
ZSCAN18
MGC2752
TSEN34
MBOAT7
FKRP
ZSCAN5A
LENG1
LILRP2
LILRA6
ZNF329
TBC1D17
ZNF419
ISOC2
MYH14
ZNF665
ZNF552
ZNF671
ZNF613
ZNF702P
ZNF606
ZNF614
FUZ
RSPH6A
ZNF611
MED25
BCL2L12
GRWD1
CCDC8
ZNF541
SYT3
AKT1S1
ZNF528
BRSK1
SNORD35B
ZNF347
ZNF577
SUV420H2
C19orf48
ZBTB45
ZNF587
FIZ1
GALP
SIGLEC10
SIGLEC12
ZNF628
KIR3DX1
ZNF551
ZNF616
ZNF766
ZNF468
ZNF160
CTU1
ZNF835
ZNF765
NLRP12
MYADM
ZNF845
CCDC114
DKFZp434J0226
ACPT
CGB5
CGB7
LRRC4B
LENG9
CGB8
GNG8
BIRC8
FAM71E1
RDH13
PTH2
ZIM3
SIGLEC11
CGB1
CGB2
LMTK3
LENG8
KIR3DL3
ZNF837
CLDND2
ZNF816
ZNF543
COX6B2
OSCAR
ZNF813
JOSD2
IZUMO2
CPT1C
ALDH16A1
NTN5
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
VSIG10L
LOC147646
LINC00085
ZNF480
ZNF534
ZNF578
ERVV-1
LOC147670
C19orf18
ZNF418
ZNF417
ZNF548
TMEM190
TMC4
LOC147804
ZNF524
ZNF784
CCDC155
DACT3
SIX5
IGFL2
NLRP4
ZNF542
ZNF582
ZNF583
CDC42EP5
ZNF836
ZNF610
ZNF600
ZNF320
ZNF497
ZNF550
ZNF579
ZNF114
ZNF525
SPACA4
NLRP7
C19orf76
ZNF584
ZSCAN4
NLRP11
TMEM86B
PRR24
ZNF549
NAPSB
IL4I1
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
TPRX1
MAMSTR
IZUMO1
C19orf63
MGC45922
KLK9
SIGLECP3
C19orf75
ZNF615
ZNF841
LOC284379
VSTM1
TMEM150B
FAM71E2
VN1R2
VN1R4
NLRP9
MYPOP
NANOS2
C19orf81
ZNF677
RFPL4A
ZSCAN5B
ZSCAN22
ZNF530
C19orf51
LILRA5
IGFL1
ZNF773
LOC386758
LOC388553
IGFL3
ZNF808
ZNF761
TMEM238
ZNF470
ZNF749
ZNF324B
ZNF805
ZNF321P
SIGLEC16
FLJ26850
ZNF880
ZNF772
IGLON5
MIRLET7E
MIR125A
MIR150
MIR99B
TARM1
MIR371A
MIR372
MIR373
IGFL4
A1BG-AS1
DPRX
DUXA
ASPDH
MIR512-1
MIR512-2
MIR498
MIR520E
MIR515-1
MIR519E
MIR520F
MIR515-2
MIR519C
MIR520A
MIR526B
MIR519B
MIR525
MIR523
MIR518F
MIR520B
MIR518B
MIR526A1
MIR520C
MIR518C
MIR524
MIR517A
MIR519D
MIR521-2
MIR520D
MIR517B
MIR520G
MIR516B2
MIR526A2
MIR518E
MIR518A1
MIR518D
MIR516B1
MIR518A2
MIR517C
MIR520H
MIR521-1
MIR522
MIR519A1
MIR527
MIR516A1
MIR516A2
MIR519A2
KLKP1
LOC646508
SBK2
LOC646862
SEC1
SNORD23
SNORD88A
SNORD88B
SNORD88C
MIR643
RPL13AP5
CCDC61
CEACAM18
SHISA7
FLJ30403
ZNF814
MIR769
SIGLEC14
MIMT1
MIR935
SNAR-G1
SNAR-F
SNAR-A1
SNAR-A2
SNAR-A12
LOC100128252
LOC100128398
LOC100129083
SGK110
BSPH1
LOC100131691
PEG3-AS1
SNAR-A3
SNAR-A5
SNAR-A7
SNAR-A11
SNAR-A9
SNAR-A4
SNAR-A6
SNAR-A8
SNAR-A13
SNAR-A10
SNAR-B2
SNAR-C2
SNAR-C4
SNAR-E
SNAR-C5
SNAR-B1
SNAR-C1
SNAR-C3
SNAR-D
SNAR-G2
SNAR-A14
ERVV-2
ZNF587B
MIR1283-2
MIR1323
MIR1283-1
MIR3191
MIR3190
MIR320E
MIR4324
LOC100505681
LOC100505812
LOC100506012
LOC100506033
LOC100506068
LOC100507003
ZNF865
ZNF816-ZNF321P
MIR4754
MIR4752
MIR371B
MIR4749
MIR4750
MIR4751

Genes in Wide Peak

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

Table S59. 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
GPR31
IGF2R
KIF25
LPA
MAS1
MAP3K4
OPRM1
PARK2
PCMT1
PDCD2
PLG
PSMB1
RPS6KA2
SLC22A1
SLC22A3
SLC22A2
SOD2
T
TBP
TCP1
TCP10
TCTE3
DYNLT1
THBS2
EZR
VIP
RNASET2
SYNJ2
LATS1
QKI
WTAP
AKAP12
UST
PDE10A
RAB32
KATNA1
SCAF8
TAB2
SASH1
SYNE1
MTHFD1L
IPCEF1
TIAM2
C6orf123
FBXO5
RGS17
DLL1
MRPL18
CLDN20
NOX3
TFB1M
SNX9
BRP44L
UNC93A
MTRF1L
RMND1
PHF10
C6orf70
AGPAT4
TULP4
PLEKHG1
ARID1B
TMEM181
ZBTB2
SMOC2
ULBP3
C6orf211
ZDHHC14
ADGB
FRMD1
AGPAT4-IT1
C6orf208
C6orf97
MYCT1
ULBP2
ULBP1
LPAL2
PPP1R14C
RSPH3
TTLL2
FAM120B
FNDC1
LRP11
SERAC1
PPIL4
LINC00473
SYTL3
SFT2D1
C6orf72
TAGAP
STXBP5
PACRG
RAET1E
CNKSR3
RAET1L
PNLDC1
LOC154449
DACT2
C6orf118
OSTCP1
WDR27
LOC285796
PRR18
ZC3H12D
NUP43
RAET1G
SUMO4
C6orf120
SAMD5
IYD
DKFZp451B082
TCP10L2
LINC00242
GTF2H5
LOC441177
RAET1K
MLLT4-AS1
SNORA20
SNORA29
LOC729176
LOC729178
TMEM242
LOC729603
HGC6.3
LOC100128176
LOC100129518
C6orf99
LOC100289495
MIR1913
MIR3918
MIR3939
MIR3692
CAHM
MIR4466
MIR4644
LOC100652739

Genes in Wide Peak

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

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

Genes
ZMYND11
DIP2C
LARP4B
TUBB8
C10orf108

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
ANP32C
MARCH1
C4orf39
TRIM61
LOC100505989
LOC100506013

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-3181
NOD2

Genes in Wide Peak

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

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

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

Genes in Wide Peak

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

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

Genes
CBFA2T3
FANCA
MAF
hsa-mir-1910
hsa-mir-3182
AFG3L1P
APRT
C16orf3
CA5A
CDH13
CDH15
COX4I1
CTRB1
CYBA
DPEP1
FOXF1
FOXL1
FOXC2
GALNS
GAS8
GCSH
GLG1
HSBP1
HSD17B2
IRF8
KARS
MC1R
CHST6
MVD
CHMP1A
PLCG2
PSMD7
RPL13
SPG7
GAN
SLC7A5
CDK10
MBTPS1
TAF1C
USP10
BCAR1
C16orf7
KIAA0513
PIEZO1
ATP2C2
CLEC3A
MPHOSPH6
COX4NB
TUBB3
CFDP1
PRDM7
GABARAPL2
MON1B
TCF25
ZCCHC14
KIAA0182
ATMIN
COTL1
MLYCD
ADAT1
CHST5
CPNE7
IL17C
ANKRD11
OSGIN1
GINS2
TRAPPC2L
WWOX
BCMO1
TERF2IP
NECAB2
KLHDC4
DEF8
BANP
RFWD3
ZDHHC7
CENPN
C16orf61
JPH3
VAT1L
KIAA1609
WFDC1
MTHFSD
DBNDD1
FA2H
TMEM231
WDR59
KLHL36
FBXO31
CMIP
CDT1
MAP1LC3B
DYNLRB2
HSDL1
CRISPLD2
SPIRE2
ZNF469
ZNRF1
CNTNAP4
CENPBD1
ZNF276
KCNG4
SDR42E1
PKD1L2
RNF166
C16orf46
DNAAF1
SPATA2L
C16orf55
ZC3H18
CDYL2
TMEM170A
SLC38A8
SLC22A31
FLJ30679
LOC146513
ZFPM1
ADAD2
ZFP1
ADAMTS18
MGC23284
LINC00311
LDHD
MLKL
ZNF778
ACSF3
LINC00304
LOC283922
NUDT7
SNAI3
FAM92B
CTU2
PABPN1L
LOC400548
LOC400550
LOC400558
C16orf74
CTRB2
CLEC18B
SNORD68
LOC727710
LOC732275
LOC100128881
LOC100129617
LOC100130015
SYCE1L
LOC100287036
MIR1910
MIR3182
C16orf95
MIR4720
MIR4722
MIR4719

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.12.

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

Genes
LCK
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
hsa-mir-4254
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
ALPL
RERE
BAI2
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
COL16A1
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
MEGF6
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FABP3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
HCRTR1
HDAC1
ZBTB48
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MATN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SRSF4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
PTP4A2
SNHG3
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
AKR7A2
ALDH4A1
EIF3I
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
SNRNP40
C1orf38
H6PD
ISG15
PLCH2
SDC3
CROCC
PUM1
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
KHDRBS1
GMEB1
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
TMEM50A
KPNA6
STX12
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
RNU11
HSPB7
ARHGEF16
AHDC1
SMPDL3B
PRO0611
LINC00339
SSU72
UBIAD1
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF593
MECR
SDF4
MRTO4
YTHDF2
ZCCHC17
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
BSDC1
XKR8
TMEM39B
ARHGEF10L
VPS13D
ATAD3A
TMEM57
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
IQCC
DNAJC11
RCC2
AJAP1
TMEM234
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
TINAGL1
PLA2G2F
CEP85
NMNAT1
VWA1
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
PHACTR4
C1orf135
CCDC28B
EFHD2
MMEL1
RSG1
OR4F5
NKAIN1
MUL1
NOL9
LIN28A
AGMAT
LINC00115
MORN1
FAM110D
DHDDS
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
TSSK3
CCNL2
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
FAM167B
C1orf170
CROCCP2
SYTL1
IGSF21
SNHG12
KIAA1751
KIAA2013
THAP3
C1orf201
SPOCD1
UBXN11
C1orf158
FBXO44
ATPIF1
CROCCP3
FHAD1
LOC115110
RAB42
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
DCDC2B
LOC149086
PDIK1L
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
TXLNA
C1orf126
ATAD3C
AKR7L
LOC254099
TTLL10
TMCO4
ZNF683
NPHP4
LOC284551
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
TMEM240
TMEM52
MTMR9LP
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
SERINC2
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
CATSPER4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
RNF223
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
ANKRD65
PRAMEF7
PEF1
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA1
SNORA44
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD85
SNORD99
SNORD103A
SNORD103B
MIR551A
CDK11A
SLC35E2B
LOC728716
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100128071
LOC100129196
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
NPPA-AS1
MIR3115
MIR4253
MIR4251
MIR4252
MIR4254
MIR3917
MIR3675
ENO1-AS1
LOC100506730
LOC100506801
LOC100506963
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4420
MIR4684
MIR4689
MIR4632
MIR4417
MIR378F
RCAN3AS

Genes in Wide Peak

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

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

Genes
PTPRD
TYRP1
MPDZ
LURAP1L
FLJ41200

Genes in Wide Peak

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

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

Genes
KCNIP4
KCNIP4-IT1

Genes in Wide Peak

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

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

Genes
NKX2-1
CCNB1IP1
hsa-mir-3172
hsa-mir-624
hsa-mir-3171
hsa-mir-4307
hsa-mir-208b
hsa-mir-1201
ANG
APEX1
ARHGAP5
BCL2L2
CEBPE
CFL2
CMA1
LTB4R
CTSG
DAD1
COCH
FKBP3
FOXG1
GPR33
GZMH
GZMB
FOXA1
HNRNPC
CTAGE5
MMP14
MYH6
MYH7
NEDD8
NFATC4
NFKBIA
NOVA1
PNP
NRL
OXA1L
PAX9
PCK2
PNN
PRKD1
PSMA6
PSMB5
PSME1
PSME2
RABGGTA
RNASE1
RNASE2
RNASE3
RNASE4
RNASE6
SALL2
SRP54
SSTR1
TEP1
TGM1
PABPN1
GEMIN2
AP1G2
SLC7A7
CPNE6
AKAP6
KIAA0391
TOX4
REC8
PARP2
DHRS2
EFS
IRF9
PRMT5
SEC23A
TM9SF1
EDDM3A
DHRS4
RIPK3
AP4S1
BAZ1A
SUPT16H
ACIN1
FAM179B
SCFD1
KHNYN
SLC7A8
HECTD1
HEATR5A
NGDN
LRP10
NKX2-8
TINF2
OR10G3
OR10G2
OR4E2
CIDEB
CHMP4A
STXBP6
STRN3
SLC39A2
FAM158A
ZNF219
GMPR2
SLC22A17
MBIP
KLHL28
HAUS4
PPP2R3C
PRPF39
C14orf119
RNF31
RBM23
MIS18BP1
C14orf167
G2E3
OSGEP
ARHGEF40
EAPP
METTL3
LTB4R2
SDR39U1
RPGRIP1
NDRG2
NYNRIN
HOMEZ
CHD8
FANCM
SNX6
C14orf93
ABHD4
NPAS3
EDDM3B
CDH24
METTL17
IL25
THTPA
OR4K5
OR11H2
OR4K1
IPO4
NUBPL
DCAF11
OR4K15
FSCB
BRMS1L
JPH4
RNASE7
INSM2
ARHGAP5-AS1
RAB2B
AJUBA
ZFHX2
RPPH1
SLC25A21
LRRC16B
PPP1R3E
TMEM55B
TTC5
EGLN3
C14orf126
DHRS1
CMTM5
MIA2
C14orf28
TRAPPC6B
RNASE11
TPPP2
RNASE8
MRPL52
PSMB11
OR4K14
OR4L1
OR11H6
KLHL33
RPL10L
MIPOL1
MDP1
LRFN5
CLEC14A
FITM1
REM2
MDGA2
C14orf21
SPTSSA
ADCY4
RALGAPA1
SFTA3
FBXO33
IGBP1P1
LOC283547
LOC283624
TSSK4
FAM177A1
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
SNORD127
SNORD126
MIR208B
LOC100129794
LOC100288846
MIR4307
MIR548Y
LOC100505967
LOC100506071
LOC100506433
NEDD8-MDP1
BCL2L2-PABPN1
MIR4503
MIR548AI
MIR4707

Genes in Wide Peak

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

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

Genes
APC
CD74
EBF1
ITK
NPM1
PDGFRB
PIK3R1
TLX3
NSD1
RANBP17
hsa-mir-340
hsa-mir-1229
hsa-mir-4281
hsa-mir-1271
hsa-mir-585
hsa-mir-218-2
hsa-mir-103-1-as
hsa-mir-146a
hsa-mir-3142
hsa-mir-1303
hsa-mir-3141
hsa-mir-1294
hsa-mir-378
hsa-mir-145
hsa-mir-584
hsa-mir-874
hsa-mir-886
hsa-mir-1289-2
hsa-mir-1244-2
hsa-mir-548f-3
hsa-mir-548p
hsa-mir-583
hsa-mir-2277
hsa-mir-9-2
hsa-mir-4280
ADRA1B
ADRB2
ANXA6
TRIM23
ARSB
ATOX1
ALDH7A1
BHMT
BNIP1
BTF3
CAMK4
CAMK2A
CAMLG
CANX
CAST
CCNB1
CCNG1
CCNH
CD14
CDC25C
CDK7
CDO1
CDX1
CETN3
CHD1
CKMT2
AP3S1
CLTB
COX7C
CRHBP
HAPLN1
CSF1R
CSF2
CSNK1A1
CSNK1G3
VCAN
NKX2-5
CTNNA1
DBN1
DMXL1
DHFR
DIAPH1
DOCK2
DPYSL3
DRD1
SLC26A2
HBEGF
DUSP1
EFNA5
EGR1
ETF1
F2R
F2RL1
F2RL2
F12
FABP6
FAT2
FBN2
FER
FGF1
FGFR4
FOXD1
FOXI1
FLT4
GABRA1
GABRA6
GABRB2
GABRG2
GABRP
GDF9
GFRA3
GLRA1
GLRX
GM2A
GRK6
GPX3
GRIA1
NR3C1
GRM6
GTF2H2
HARS
HEXB
HINT1
HK3
HMGCR
HMMR
HNRNPAB
HNRNPH1
HRH2
HSD17B4
HSPA4
HSPA9
NDST1
HTR1A
HTR4
IK
IL3
IL4
IL5
IL9
IL12B
IL13
IRF1
KCNMB1
KCNN2
TNPO1
LCP2
LECT2
LMNB1
LNPEP
LOX
LTC4S
CD180
SMAD5
MAN2A1
MAP1B
MCC
MEF2C
MFAP3
MGAT1
MSH3
MSX2
NAIP
NDUFA2
NEUROG1
NPY6R
PAM
PCDH1
PCDHGC3
PCSK1
PDE6A
PFDN1
PGGT1B
PITX1
PMCHL2
POU4F3
PPIC
PPP2CA
PPP2R2B
MAPK9
PROP1
PURA
RAD17
RARS
RASA1
RASGRF2
RPS14
RPS23
SGCD
SKP1
SLC6A7
SLC12A2
SLC34A1
SLC22A4
SLC22A5
SLIT3
SMN1
SMN2
SNCB
SNX2
SPARC
SPINK1
SPOCK1
SRP19
STK10
TAF7
TAF9
TBCA
TCF7
ZNF354A
TCOF1
NR2F1
TGFBI
THBS4
TTC1
UBE2B
UBE2D2
VDAC1
WNT8A
XRCC4
ST8SIA4
REEP5
SERF1A
NME5
ENC1
AP3B1
PDLIM4
STC2
PDE8B
EIF4EBP3
PCDHGB4
CDC23
ADAM19
FGF18
HDAC3
SQSTM1
P4HA2
ATP6V0E1
ATG12
PTTG1
PDLIM7
NREP
CNOT8
RAB9BP1
HAND1
MED7
HOMER1
MYOT
ADAMTS2
SCAMP1
NRG2
CXCL14
H2AFY
SMAD5-AS1
RNF14
CARTPT
SNCAIP
TTC37
CLINT1
PCDHGA8
PCDHA9
ZFYVE16
MATR3
MAML1
KIAA0141
JAKMIP2
PJA2
DDX46
GFPT2
SLC23A1
GNPDA1
SRA1
EDIL3
COL4A3BP
RAD50
KIF20A
G3BP1
LHFPL2
CWC27
APBB3
TNIP1
GNB2L1
NSA2
SLU7
POLR3G
RGS14
IQGAP2
SEC24A
CPLX2
C5orf4
FAM114A2
BRD8
TCERG1
BTNL3
HNRNPA0
LMAN2
SPINK5
SMA4
SMA5
SOX30
KIF3A
ADAMTS6
MGAT4B
B4GALT7
SYNPO
RHOBTB3
RNF44
ABLIM3
ELL2
SV2C
HMGXB3
TBC1D9B
ARHGAP26
FSTL4
MRPS27
ATP10B
N4BP3
SEPT8
FAF2
PPIP5K2
WWC1
FBXW11
ACSL6
PHF15
LARP1
PPWD1
HARS2
OTP
ZNF346
SSBP2
BHMT2
TNFAIP8
GEMIN5
PCDHGA12
LRRTM2
FAM169A
CCDC69
PCDHB5
FBXL21
KLHL3
TSPAN17
OR4F3
HAVCR1
SNORD63
SNORA74A
RNU5E-1
RNU5D-1
CYFIP2
PKD2L2
UQCRQ
AFF4
PRELID1
IL17B
DIMT1
MAT2B
SLC27A6
SNX24
MRPL22
PCDHB1
DMGDH
KCNIP1
ZNF354C
TMED7
ISOC1
RPL26L1
SAR1B
C5orf45
DCTN4
IPO11
MZB1
PAIP2
CDKL3
PCDH12
GCNT4
FAM13B
FAM53C
REEP2
PRR16
COMMD10
POLK
DDX41
NOP16
LARS
CXXC5
HMP19
UIMC1
RAPGEF6
ERAP1
KDM3B
PHAX
RAB24
RBM27
NEURL1B
FLJ11235
FAM193B
SGTB
PCDHB18
PCDHB17
TMED9
ZCCHC10
CDHR2
GIN1
WDR55
ANKHD1
CCDC99
THG1L
AGGF1
WDR41
TMCO6
TRIM36
GALNT10
NHP2
RBM22
RIOK2
BDP1
RNF130
ERBB2IP
PCDHGC5
PCDHGC4
PCDHGB7
PCDHGB6
PCDHGB5
PCDHGB3
PCDHGB2
PCDHGB1
PCDHGA11
PCDHGA10
PCDHGA9
PCDHGA7
PCDHGA6
PCDHGA5
PCDHGA4
PCDHGA3
PCDHGA2
PCDHGA1
PCDHGB8P
PCDHB15
PCDHB14
PCDHB13
PCDHB12
PCDHB11
PCDHB10
PCDHB9
PCDHB8
PCDHB7
PCDHB6
PCDHB4
PCDHB3
PCDHB2
PCDHAC2
PCDHAC1
PCDHA13
PCDHA12
PCDHA11
PCDHA10
PCDHA8
PCDHA7
PCDHA6
PCDHA5
PCDHA4
PCDHA3
PCDHA2
PCDHA1
VTRNA1-3
VTRNA1-2
VTRNA1-1
NMUR2
FEM1C
C5orf15
CDC42SE2
TRPC7
KIAA1191
ERGIC1
CLK4
ODZ2
CNOT6
NLN
ZNF608
KCTD16
SEMA6A
ARRDC3
PCDHB16
ANKRA2
HMHB1
C5orf54
MCCC2
EPB41L4A
CENPK
ERAP2
RGNEF
SIL1
GMCL1P1
ARAP3
RMND5B
FBXL17
YTHDC2
SLC30A5
CENPH
GRAMD3
PCYOX1L
CCNJL
SH3TC2
PANK3
SAP30L
TXNDC15
MCTP1
PTCD2
BTNL8
DOK3
C5orf44
ZFP2
RUFY1
CPEB4
PRR7
NDFIP1
OR4F16
FBXO38
YIPF5
TRIM7
TIGD6
SPRY4
MXD3
NUDT12
SLC4A9
ATG10
SLC25A2
SPATA9
TSSK1B
FAM172A
PCDHB19P
GPR98
PCBD2
UTP15
ZCCHC9
PSD2
ANKRD32
THOC3
ZBED3
GFM2
C5orf32
MEGF10
SPINK7
SPZ1
TRIM52
HAVCR2
AGXT2L2
C5orf62
TSLP
FCHSD1
UNC5A
C5orf30
LYRM7
TRIM41
SLC25A46
BOD1
CDKN2AIPNL
COL23A1
TIMD4
ZNF300
MYOZ3
UBTD2
MRPS36
ATP6AP1L
SCGB3A1
PRDM6
FTMT
SFXN1
FNIP1
SLC35A4
GPRIN1
PWWP2A
C1QTNF2
EPB41L4A-AS1
MARCH3
FCHO2
LYSMD3
LEAP2
SCGB3A2
ZNF354B
SLCO6A1
C5orf47
PPARGC1B
PRRC1
JMY
C5orf58
ZNF474
OR2Y1
POU5F2
AFAP1L1
GRPEL2
TMEM171
TMEM174
LSM11
POC5
GPR151
STARD4
WDR36
ZNF300P1
NUDCD2
UBLCP1
ACOT12
SOWAHA
SHROOM1
C5orf24
SREK1
C5orf20
SLC36A2
SPINK13
C5orf41
CEP120
SLC25A48
TMEM167A
MBLAC2
TMEM161B
SRFBP1
LOC153469
ZMAT2
MARVELD2
BTNL9
ARSK
FAM81B
CCDC112
PPP1R2P3
FAM71B
PRELID2
SH3RF2
PLAC8L1
RNF145
PAPD4
DCP2
LIX1
ZNF366
FAM151B
S100Z
ADAMTS19
HIGD2A
SPATA24
DNAJC18
FAM153B
LOC202181
CCDC125
C5orf27
CMYA5
STK32A
AQPEP
SLC36A1
EIF4E1B
RASGEF1C
ANKRD31
SERINC5
LOC257358
EFCAB9
SH3PXD2B
LOC285593
FAM153A
ARL10
KIAA0825
GPR150
DTWD2
RELL2
NBPF22P
LOC285626
LOC285627
LOC285629
SLC36A3
KIF4B
OR2V2
RNF180
SREK1IP1
ZNF454
C5orf60
RGMB
RFESD
CHSY3
LOC340037
TMEM173
FAM170A
LOC340073
LOC340074
ARSI
ANKRD34B
PFN3
ZNF879
IRGM
FBLL1
FAM174A
MTX3
CATSPER3
NIPAL4
SLCO4C1
TICAM2
DND1
MAST4
C5orf25
FLJ38109
C5orf48
LOC389332
C5orf65
C5orf46
ARHGEF37
RGS7BP
C5orf63
SPINK6
ANKHD1-EIF4EBP3
MIR103A1
MIR143
MIR145
MIR146A
MIR218-2
MIR9-2
SPINK14
FNDC9
CRSP8P
FLJ42709
C5orf56
FLJ16171
MIR340
IGIP
TIFAB
FLJ35946
LOC553103
CTXN3
SNORD95
SNORD96A
ECSCR
TMEM232
LOC643201
GRXCR2
SPINK9
ZFP62
LOC644100
FLJ33630
LOC644936
CCNI2
LINC00461
CBY3
LOC647859
GUSBP3
GTF2H2B
FAM153C
SNORA13
SCARNA18
SNORA47
SNORA74B
MIR583
MIR585
SNHG4
MIR143HG
GTF2H2C
LOC728342
SERF1B
LOC728554
LOC728723
LOC729080
AACSP1
LOC729678
OR4F29
GTF2H2D
GUSBP9
VTRNA2-1
MIR874
LOC100129716
LRRC70
LOC100131067
FAM196B
LOC100132062
LOC100132287
FAM159B
LOC100133050
LOC100133331
LOC100170939
C5orf52
LOC100268168
LOC100272216
LOC100289230
LOC100289673
MIR1289-2
MIR1229
MIR103B1
MIR1244-1
TMED7-TICAM2
NCRUPAR
LOC100303749
MIR2277
MIR1244-3
MIR1244-2
MIR4280
MIR3142
MIR3141
MIR4281
MTRNR2L2
MIR3607
MIR3655
MIR3660
MIR3912
MIR3936
MIR3661
LOC100505658
LOC100505678
LOC100505841
LOC100505894
OCLN
LOC100507387
MIR4804
MIR4633
MIR4634
MIR4461
MIR3977
MIR4460
MIR4638
MIR4803
MIR378E
LOC100859930

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.23.

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

Genes
LCK
PAX7
RPL22
SDHB
ARID1A
TNFRSF14
PRDM16
MDS2
hsa-mir-4254
hsa-mir-1976
hsa-mir-3115
hsa-mir-4253
hsa-mir-1256
hsa-mir-1290
hsa-mir-1273d
hsa-mir-34a
hsa-mir-4252
hsa-mir-551a
hsa-mir-4251
hsa-mir-429
hsa-mir-1302-2
ALPL
RERE
BAI2
C1QA
C1QB
C1QC
CA6
CAPZB
CASP9
RUNX3
TNFRSF8
CDA
CDK11B
CDC42
CD52
RCC1
CLCN6
CLCNKA
CLCNKB
CNR2
COL16A1
CORT
DDOST
DFFA
DFFB
DVL1
E2F2
ECE1
MEGF6
EPHA2
ENO1
EPB41
EPHA8
EPHB2
EXTL1
EYA3
FABP3
FGR
MTOR
FUCA1
IFI6
GABRD
GALE
GNB1
SFN
GPR3
HCRTR1
HDAC1
ZBTB48
HMGN2
HMGCL
HSPG2
HTR1D
HTR6
ID3
TNFRSF9
STMN1
MATN1
MFAP2
MTHFR
NBL1
NPPA
NPPB
OPRD1
PAFAH2
PEX10
PEX14
PGD
PIK3CD
PLA2G2A
PLA2G5
PLOD1
EXOSC10
PPP1R8
PRKCZ
PTAFR
RAP1GAP
RHCE
RHD
RPA2
RPL11
RPS6KA1
RSC1A1
SCNN1D
SRSF4
SKI
SLC2A5
SLC9A1
SRM
TAF12
TCEA3
TCEB3
TNFRSF1B
TP73
TNFRSF4
ZBTB17
SLC30A2
LUZP1
PRDM2
LAPTM5
PTP4A2
SNHG3
NR0B2
MMP23B
MMP23A
KCNAB2
FCN3
AKR7A2
ALDH4A1
EIF3I
EIF4G3
TNFRSF25
TNFRSF18
PER3
MAP3K6
DHRS3
VAMP3
SNRNP40
C1orf38
H6PD
ISG15
PLCH2
SDC3
CROCC
PUM1
CEP104
KLHL21
SLC35E2
ZBTB40
MFN2
PTPRU
CELA3A
WASF2
ANGPTL7
HNRNPR
SRRM1
CNKSR1
UBE4B
MAD2L2
PDPN
KHDRBS1
GMEB1
NUDC
MASP2
SRSF10
UTS2
RER1
RCAN3
MST1P2
MST1P9
PADI2
LYPLA2
PARK7
CTRC
ACOT7
DNAJC8
CLSTN1
AKR7A3
SPEN
KDM1A
WDTC1
KIAA0090
KIF1B
PLEKHM2
OTUD3
KAZN
CAMTA1
DNAJC16
UBR4
ATP13A2
TARDBP
CELA3B
ICMT
PADI4
TMEM50A
KPNA6
STX12
CLIC4
SYF2
CHD5
C1orf144
LDLRAP1
NOC2L
FBXO2
FBXO6
PLA2G2D
OR4F3
RNU11
HSPB7
ARHGEF16
AHDC1
SMPDL3B
PRO0611
LINC00339
SSU72
UBIAD1
PADI1
PLA2G2E
WRAP73
SLC45A1
HP1BP3
CELA2B
ZNF593
MECR
SDF4
MRTO4
YTHDF2
ZCCHC17
PADI3
ERRFI1
WNT4
FBXO42
RNF186
MXRA8
HES2
GPN2
FBLIM1
MED18
PQLC2
CASZ1
TRNAU1AP
CPSF3L
C1orf159
AURKAIP1
MRPL20
AIM1L
TMEM51
BSDC1
XKR8
TMEM39B
ARHGEF10L
VPS13D
ATAD3A
TMEM57
PANK4
CAMK2N1
ASAP3
PNRC2
PIGV
NBPF1
NECAP2
IQCC
DNAJC11
RCC2
AJAP1
TMEM234
FAM54B
CTNNBIP1
C1orf63
AGTRAP
PITHD1
MAN1C1
NIPAL3
SEPN1
TP73-AS1
PLEKHG5
LRRC47
PTCHD2
KIF17
HES4
GRHL3
IL22RA1
MIIP
CELA2A
GPATCH3
TINAGL1
PLA2G2F
CEP85
NMNAT1
VWA1
PINK1
MARCKSL1
PRAMEF1
PRAMEF2
NADK
PHACTR4
C1orf135
CCDC28B
EFHD2
MMEL1
RSG1
OR4F5
NKAIN1
MUL1
NOL9
LIN28A
AGMAT
LINC00115
MORN1
FAM110D
DHDDS
GPR157
SPSB1
GLTPD1
ZNF436
TAS1R2
TAS1R1
OR4F16
ACTL8
TSSK3
CCNL2
SH3BGRL3
SESN2
ESPN
TAS1R3
ATAD3B
TMEM222
PLEKHN1
USP48
NBPF3
ZDHHC18
SLC25A33
DDI2
LZIC
TRIM63
FAM167B
C1orf170
CROCCP2
SYTL1
IGSF21
SNHG12
KIAA1751
KIAA2013
THAP3
C1orf201
SPOCD1
UBXN11
C1orf158
FBXO44
ATPIF1
CROCCP3
FHAD1
LOC115110
RAB42
FAM46B
RBP7
ACAP3
UBE2J2
C1orf172
LRRC38
AADACL3
PUSL1
B3GALT6
IFFO2
TPRG1L
FAM213B
MYOM3
KLHDC7A
VWA5B1
UBXN10
ARHGEF19
ACTRT2
MIB2
C1orf127
SAMD11
LOC148413
PHF13
CCDC27
C1orf213
DCDC2B
LOC149086
PDIK1L
C1orf64
SLC2A7
CALML6
IL28RA
FAM43B
PAQR7
FAM76A
TMEM201
C1orf86
TXLNA
C1orf126
ATAD3C
AKR7L
LOC254099
TTLL10
TMCO4
ZNF683
NPHP4
LOC284551
FAM41C
LOC284632
LOC284661
SLC25A34
ESPNP
C1orf174
KLHL17
TMEM240
TMEM52
MTMR9LP
LOC339505
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
SERINC2
FAM131C
PADI6
C1orf187
SPATA21
AGRN
APITD1
CATSPER4
GPR153
FAM132A
HES5
LOC388588
RNF207
TMEM82
TRNP1
CD164L2
HES3
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF18
PRAMEF17
PLA2G2C
TMEM200B
PRAMEF4
PRAMEF13
SH2D5
C1orf130
RNF223
PRAMEF3
LDLRAD2
MIR200A
MIR200B
MIR34A
FLJ42875
PRAMEF11
PRAMEF6
LOC440563
UQCRHL
MINOS1
ANKRD65
PRAMEF7
PEF1
MIR429
FAM138F
LOC643837
TMEM88B
C1orf233
LOC644961
C1orf200
PRAMEF19
PRAMEF20
FAM138A
LOC646471
LOC649330
LOC653566
PRAMEF22
PRAMEF15
WASH7P
PRAMEF16
SCARNA1
SNORA44
SNORA61
SNORA59B
SNORA59A
SNORA16A
SNORD85
SNORD99
SNORD103A
SNORD103B
MIR551A
CDK11A
SLC35E2B
LOC728716
LOC729059
PRAMEF14
FLJ37453
LOC729737
OR4F29
LOC100128071
LOC100129196
LOC100129534
LOC100130417
LOC100132062
LOC100132287
LOC100133331
LOC100133445
LOC100133612
DDX11L1
TTC34
LOC100288069
MIR1976
NPPA-AS1
MIR3115
MIR4253
MIR4251
MIR4252
MIR4254
MIR3917
MIR3675
ENO1-AS1
LOC100506730
LOC100506801
LOC100506963
APITD1-CORT
C1orf151-NBL1
MIR4695
MIR4420
MIR4684
MIR4689
MIR4632
MIR4417
MIR378F
RCAN3AS

Genes in Wide Peak

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

Table S72. 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
ACACB
ACADS
APAF1
ARL1
ASCL1
ATP2A2
ATP2B1
SCARB1
CMKLR1
COX6A1
CRY1
DAO
DCN
EPYC
DTX1
DUSP6
EIF2B1
ELK3
STX2
GOLGA3
GTF2H3
HAL
HPD
IGF1
LTA4H
LUM
KITLG
MMP17
MSI1
MVK
MYBPC1
MYL2
NFYB
NOS1
NTS
OAS1
OAS2
OAS3
P2RX4
P2RX7
PEBP1
PAH
CDK17
SLC25A3
PLA2G1B
PMCH
POLE
PPP1CC
PRKAB1
PSMD9
PXMP2
PXN
RAN
RFC5
RFX4
RPL6
RPLP0
CLIP1
ATXN2
SELPLG
SFSWAP
SNRPF
TBX5
TBX3
HNF1A
TDG
TMPO
NR2C1
HSP90B1
TXNRD1
UBC
UBE2N
UNG
ZNF10
ZNF26
ZNF84
ZNF140
ALX1
CDK2AP1
BRAP
ULK1
EEA1
RASAL1
MAPKAPK5
DENR
OASL
DYNLL1
SRSF9
GALNT4
CRADD
HRK
ADAM1
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
RAB35
SNRNP35
KERA
PRDM4
CIT
PWP1
FICD
NUDT4
FZD10
MLXIP
RPH3A
P2RX2
FBXO21
SETD1B
UHRF1BP1L
ANKLE2
CUX2
KIAA1033
MED13L
SIRT4
ABCB9
ISCU
RIMBP2
ATP6V0A2
CORO1C
MGAT4C
FBXW8
HSPB8
HCAR1
UTP20
MRPL42
IFT81
FAM216A
HCFC2
SYCP3
CHST11
GALNT9
CCDC53
CCDC41
GPN3
GLTP
C12orf47
ARL6IP4
TAOK3
POP5
ANAPC5
ANAPC7
TRIAP1
NT5DC3
VPS29
TPCN1
SSH1
RHOF
VSIG10
TESC
PARPBP
SLC6A15
RIC8B
APPL2
SBNO1
DRAM1
SVOP
STAB2
VEZT
GOLGA2P5
ZCCHC8
SCYL2
POLR3B
CHFR
FGD6
WSB2
NDUFA12
DIABLO
ANKS1B
CHPT1
TMCC3
PITPNM2
EP400
DHX37
FBRSL1
DDX55
NTN4
TRPV4
LHX5
SUDS3
ACTR6
C12orf43
VPS33A
RSRC2
AACS
NUP37
DDX54
NOC4L
GNPTAB
B3GNT4
TCTN1
OGFOD2
VPS37B
C12orf49
TCTN2
NAA25
SLC24A6
CEP290
RNF34
CCDC92
MTERFD3
PUS1
ACAD10
GLT8D2
KCTD10
USP44
SLC41A2
LRRIQ1
C12orf26
TCHP
COQ5
HVCN1
SRRM4
CCDC62
KDM2B
UNC119B
USP30
ORAI1
RNFT2
C12orf34
C12orf52
MGC14436
ANKRD13A
TMEM116
UBE3B
C12orf23
C12orf29
C12orf65
TMEM132C
CCDC64
SDSL
TMEM132B
IQCD
LOC116437
DEPDC4
CCDC38
C12orf45
TMEM132D
SLC15A4
NEDD1
SLC9A7P1
IKBIP
ASCL4
BTBD11
SPIC
ANO4
ALKBH2
FOXN4
SPPL3
BRI3BP
AMDHD1
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
TSPAN19
LOC144481
LOC144486
RAD9B
FAM109A
LOC144742
KRT19P2
TMTC2
TMTC3
C12orf50
ALDH1L2
SLC5A8
PPTC7
CCDC63
CCDC60
PGAM5
RILPL2
DNAH10
PLBD2
FAM71C
RMST
C12orf12
SLC17A8
GNN
LRRC43
TCP11L2
LOC255480
LOC256021
POC1B
GPR133
MORN3
GAS2L3
LINC00485
MYO1H
C12orf51
KSR2
GATC
HNF1A-AS1
DDX51
MMAB
HCAR2
LOC338758
TMEM119
LOC338799
C12orf74
EP400NL
RILPL1
C12orf42
IL31
C12orf75
CCDC42B
TMEM233
SETD8
LOC387895
MKRN9P
C12orf76
LOC400084
FLJ37505
MIR135A2
C12orf37
PLEKHG7
LOC440117
FLJ31485
NUDT4P1
MIR331
EID3
CLLU1OS
CLLU1
MIR492
MAP1LC3B2
LOC643339
LOC643770
LOC647589
SNORA49
SNORA53
MIR620
LOC728084
C12orf73
LOC728739
LOC100128191
LOC100128554
LOC100130238
LOC100131138
LOC100131733
LOC100190940
LINC00173
LOC100287944
ZNF605
MIR1827
MIR1178
MIR1251
MIR4303
MIR4304
MIR3685
MIR3612
MIR3652
MIR3922
MIR3908
LOC100505978
LOC100506649
LOC100506668
LOC100507055
LOC100507066
LOC100507091
LOC100507206
POC1B-GALNT4
ZNF664-FAM101A
MIR4498
MIR548AL
MIR4472-2
MIR4700
MIR4497

Arm-level results

Table 3. Get Full Table Arm-level significance table - 28 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.09 | -2.15 | 1 | 0.23 | 4.28 | 2.86e-05
1q | 1955 | 0.28 | 5.96 | 1.25e-08 | 0.11 | -1.53 | 1
2p | 924 | 0.26 | 3.16 | 0.00346 | 0.03 | -5.66 | 1
2q | 1556 | 0.12 | -1.68 | 1 | 0.03 | -5.53 | 1
3p | 1062 | 0.21 | 0.92 | 0.536 | 0.64 | 19.2 | 0
3q | 1139 | 0.65 | 18.4 | 0 | 0.43 | 7.96 | 3.46e-15
4p | 489 | 0.07 | -4.13 | 1 | 0.45 | 10.4 | 0
4q | 1049 | 0.04 | -4.88 | 1 | 0.38 | 8.57 | 0
5p | 270 | 0.62 | 14.7 | 0 | 0.47 | 8.07 | 1.44e-15
5q | 1427 | 0.10 | -2.19 | 1 | 0.52 | 15.5 | 0
6p | 1173 | 0.15 | -1.03 | 1 | 0.15 | -1.17 | 1
6q | 839 | 0.08 | -4.54 | 1 | 0.12 | -2.89 | 1
7p | 641 | 0.32 | 4.96 | 2.32e-06 | 0.12 | -2.84 | 1
7q | 1277 | 0.31 | 5.78 | 2.85e-08 | 0.10 | -2.55 | 1
8p | 580 | 0.19 | -0.154 | 1 | 0.54 | 13.6 | 0
8q | 859 | 0.36 | 7.33 | 1.46e-12 | 0.09 | -3.34 | 1
9p | 422 | 0.15 | -1.61 | 1 | 0.50 | 11.8 | 0
9q | 1113 | 0.14 | -1.42 | 1 | 0.32 | 5.9 | 5.99e-09
10p | 409 | 0.06 | -5.15 | 1 | 0.26 | 2.18 | 0.0357
10q | 1268 | 0.04 | -5.16 | 1 | 0.26 | 3.83 | 0.00018
11p | 862 | 0.10 | -3.56 | 1 | 0.20 | 0.395 | 0.711
11q | 1515 | 0.09 | -3.19 | 1 | 0.13 | -1.57 | 1
12p | 575 | 0.28 | 3.65 | 0.000646 | 0.04 | -5.67 | 1
12q | 1447 | 0.12 | -2.19 | 1 | 0.06 | -4.67 | 1
13q | 654 | 0.06 | -4.61 | 1 | 0.39 | 8.15 | 1.08e-15
14q | 1341 | 0.12 | -1.87 | 1 | 0.24 | 2.98 | 0.00374
15q | 1355 | 0.11 | -2.35 | 1 | 0.16 | -0.338 | 1
16p | 872 | 0.07 | -4.51 | 1 | 0.17 | -0.53 | 1
16q | 702 | 0.07 | -4.54 | 1 | 0.20 | 0.313 | 0.735
17p | 683 | 0.08 | -3.8 | 1 | 0.42 | 9.58 | 0
17q | 1592 | 0.18 | 0.857 | 0.545 | 0.14 | -1.05 | 1
18p | 143 | 0.20 | -0.671 | 1 | 0.17 | -1.43 | 1
18q | 446 | 0.14 | -2.22 | 1 | 0.25 | 1.95 | 0.0593
19p | 995 | 0.12 | -2.55 | 1 | 0.23 | 1.86 | 0.0685
19q | 1709 | 0.22 | 2.61 | 0.0148 | 0.16 | 0.238 | 0.754
20p | 355 | 0.28 | 2.99 | 0.00538 | 0.08 | -4.4 | 1
20q | 753 | 0.26 | 2.72 | 0.0116 | 0.10 | -3.47 | 1
21q | 509 | 0.08 | -4.11 | 1 | 0.35 | 6.24 | 7.66e-10
22q | 921 | 0.28 | 3.98 | 0.000191 | 0.14 | -1.58 | 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/LUSC/1551737/2.GDAC_MergeDataFiles.Finished/LUSC.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.30

- 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 282 Input Tumor Samples.

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

Figure 3. Segmented copy number profiles in the input data

Output
All Lesions File (all_lesions.conf_##.txt, where ## is the confidence level)

The all lesions file summarizes the results from the GISTIC run. It contains data about the significant regions of amplification and deletion as well as which samples are amplified or deleted in each of these regions. The identified regions are listed down the first column, and the samples are listed across the first row, starting in column 10.

Region Data

Columns 1-9 present the data about the significant regions as follows:

1. Unique Name: A name assigned to identify the region.

2. Descriptor: The genomic descriptor of that region.

3. Wide Peak Limits: The 'wide peak' boundaries most likely to contain the targeted genes. These are listed in genomic coordinates and marker (or probe) indices.

4. Peak Limits: The boundaries of the region of maximal amplification or deletion.

5. Region Limits: The boundaries of the entire significant region of amplification or deletion.

6. Q values: The Q value of the peak region.

7. Residual Q values: The Q value of the peak region after removing ('peeling off') amplifications or deletions that overlap other, more significant peak regions in the same chromosome.

8. Broad or Focal: Identifies whether the region reaches significance due primarily to broad events (called 'broad'), focal events (called 'focal'), or independently significant broad and focal events (called 'both').

9. Amplitude Threshold: Key giving the meaning of values in the subsequent columns associated with each sample.

Sample Data

Each of the analyzed samples is represented in one of the columns following the lesion data (columns 10 through end). The data contained in these columns varies slightly by section of the file. The first section can be identified by the key given in column 9 - it starts in row 2 and continues until the row that reads 'Actual Copy Change Given.' This section contains summarized data for each sample. A '0' indicates that the copy number of the sample was not amplified or deleted beyond the threshold amount in that peak region. A '1' indicates that the sample had low-level copy number aberrations (exceeding the low threshold indicated in column 9), and a '2' indicates that the sample had high-level copy number aberrations (exceeding the high threshold indicated in column 9).The second section can be identified the rows in which column 9 reads 'Actual Copy Change Given.' The second section exactly reproduces the first section, except that here the actual changes in copy number are provided rather than zeroes, ones, and twos.The final section is similar to the first section, except that here only broad events are included. A 1 in the samples columns (columns 10+) indicates that the median copy number of the sample across the entire significant region exceeded the threshold given in column 9. That is, it indicates whether the sample had a geographically extended event, rather than a focal amplification or deletion covering little more than the peak region.

Amplification Genes File (amp_genes.conf_##.txt, where ## is the confidence level)

The amp genes file contains one column for each amplification peak identified in the GISTIC analysis. The first four rows are:

1. Cytoband

2. Q value

3. Residual Q value

4. Wide Peak Boundaries

These rows identify the lesion in the same way as the all lesions file.The remaining rows list the genes contained in each wide peak. For peaks that contain no genes, the nearest gene is listed in brackets.

Deletion Genes File (del_genes.conf_##.txt, where ## is the confidence level)

The del genes file contains one column for each deletion peak identified in the GISTIC analysis. The file format for the del genes file is identical to the format for the amp genes file.

Gistic Scores File (scores.gistic)

The scores file lists the Q values [presented as -log10(q)], G scores, average amplitudes among aberrant samples, and frequency of aberration, across the genome for both amplifications and deletions. The scores file is viewable with the Genepattern SNPViewer module and may be imported into the Integrated Genomics Viewer (IGV).

Segmented Copy Number (raw_copy_number.{fig|pdf|png} )

The segmented copy number is a pdf file containing a colormap image of the segmented copy number profiles in the input data.

Amplification Score GISTIC plot (amp_qplot.{fig|pdf|png|v2.pdf})

The amplification pdf is a plot of the G scores (top) and Q values (bottom) with respect to amplifications for all markers over the entire region analyzed.

Deletion Score GISTIC plot (del_qplot.{fig|pdf|png|v2.pdf})

The deletion pdf is a plot of the G scores (top) and Q values (bottom) with respect to deletions for all markers over the entire region analyzed.

Tables (table_{amp|del}.conf_##.txt, where ## is the confidence level)

Tables of basic information about the genomic regions (peaks) that GISTIC determined to be significantly amplified or deleted. These describe three kinds of peak boundaries, and list the genes contained in two of them. The region start and region end columns (along with the chromosome column) delimit the entire area containing the peak that is above the significance level. The region may be the same for multiple peaks. The peak start and end delimit the maximum value of the peak. The extended peak is the peak determined by robust, and is contained within the wide peak reported in {amp|del}_genes.txt by one marker.

Broad Significance Results (broad_significance_results.txt)

A table of per-arm statistical results for the data set. Each arm is a row in the table. The first column specifies the arm and the second column counts the number of genes known to be on the arm. For both amplification and deletion, the table has columns for the frequency of amplification or deletion of the arm, and a Z score and Q value.

Broad Values By Arm (broad_values_by_arm.txt)

A table of chromosome arm amplification levels for each sample. Each row is a chromosome arm, and each column a sample. The data are in units of absolute copy number -2.

All Data By Genes (all_data_by_genes.txt)

A gene-level table of copy number values for all samples. Each row is the data for a gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. The copy number values in the table are in units of (copy number -2), so that no amplification or deletion is 0, genes with amplifications have positive values, and genes with deletions are negative values. The data are converted from marker level to gene level using the extreme method: a gene is assigned the greatest amplification or the least deletion value among the markers it covers.

Broad Data By Genes (broad_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only broad events with lengths greater than the broad length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

Focal Data By Genes (focal_data_by_genes.txt)

A gene-level table of copy number data similar to the all_data_by_genes.txt output, but using only focal events with lengths greater than the focal length cutoff. The structure of the file and the methods and units used for the data analysis are otherwise identical to all_data_by_genes.txt.

All Thresholded By Genes (all_thresholded.by_genes.txt)

A gene-level table of discrete amplification and deletion indicators at for all samples. There is a row for each gene. The first three columns name the gene, its NIH locus ID, and its cytoband - the remaining columns are the samples. A table value of 0 means no amplification or deletion above the threshold. Amplifications are positive numbers: 1 means amplification above the amplification threshold; 2 means amplifications larger to the arm level amplifications observed for the sample. Deletions are represented by negative table values: -1 represents deletion beyond the threshold; -2 means deletions greater than the minimum arm-level deletion observed for the sample.

Sample Cutoffs (sample_cutoffs.txt)

A table of the per-sample threshold cutoffs (in units of absolute copy number -2) used to distinguish the high level amplifications (+/-2) from ordinary amplifications (+/-1) in the all_thresholded.by_genes.txt output file. The table contains three columns: the sample identifier followed by the low (deletion) and high (amplification) cutoff values. The cutoffs are calculated as the minimum arm-level amplification level less the deletion threshold for deletions and the maximum arm-level amplification plus the amplification threshold for amplifications.

Focal Input To Gistic (focal_input.seg.txt)

A list of copy number segments describing just the focal events present in the data. The segment amplification/deletion levels are in units of (copy number -2), with amplifications positive and deletions negative numbers. This file may be viewed with IGV.

Gene Counts vs. Copy Number Alteration Frequency (freqarms_vs_ngenes.{fig|pdf})

An image showing the correlation between gene counts and frequency of copy number alterations.

Confidence Intervals (regions_track.conf_##.bed, where ## is the confidence level)

A file indicating the position of the confidence intervals around GISTIC peaks that can be loaded as a track in a compatible viewer browser such as IGV or the UCSC genome browser.

GISTIC

GISTIC identifies genomic regions that are significantly gained or lost across a set of tumors. It takes segmented copy number ratios as input, separates arm-level events from focal events, and then performs two tests: (i) identifies significantly amplified/deleted chromosome arms; and (ii) identifies regions that are significantly focally amplified or deleted. For the focal analysis, the significance levels (Q values) are calculated by comparing the observed gains/losses at each locus to those obtained by randomly permuting the events along the genome to reflect the null hypothesis that they are all 'passengers' and could have occurred anywhere. The locus-specific significance levels are then corrected for multiple hypothesis testing. The arm-level significance is calculated by comparing the frequency of gains/losses of each arm to the expected rate given its size. The method outputs genomic views of significantly amplified and deleted regions, as well as a table of genes with gain or loss scores. A more in depth discussion of the GISTIC algorithm and its utility is given in [1], [3], and [5].

CNV Description

Regions of the genome that are prone to germ line variations in copy number are excluded from the GISTIC analysis using a list of germ line copy number variations (CNVs). A CNV is a DNA sequence that may be found at different copy numbers in the germ line of two different individuals. Such germ line variations can confound a GISTIC analysis, which finds significant somatic copy number variations in cancer. A more in depth discussion is provided in [6]. GISTIC currently uses two CNV exclusion lists. One is based on the literature describing copy number variation, and a second one comes from an analysis of significant variations among the blood normals in the TCGA data set.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Beroukhim et al, Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma, Proc Natl Acad Sci U S A. Vol. 104:50 (2007)
[2] GISTIC version 1
[3] Mermel et al, GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers, Genome Biology Vol. 12:4 (2011)
[4] GISTIC version 2
[5] Beroukhim et al., The landscape of somatic copy-number alteration across human cancers, Nature Vol. 463:7283 (2010)
[6] McCarroll, S. A. et al., Integrated detection and population-genetic analysis of SNPs and copy number variation, Nat Genet Vol. 40(10):1166-1174 (2008)
[7] The Sanger Institute: Cancer Gene Census
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