PANCANCER subset with 8 initial disease types: Copy number analysis (GISTIC2)
Maintained by Dan DiCara (Broad Institute)
Overview
Introduction

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

Summary

There were 3770 tumor samples used in this analysis: 32 significant arm-level results, 39 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 - 39 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
--- | --- | --- | --- | ---
8q24.21 | 6.5005e-286 | 6.5005e-286 | chr8:128739772-128772049 | 1
7p11.2 | 1.3222e-238 | 1.3222e-238 | chr7:55063359-55095549 | 1
3q26.2 | 1.1329e-203 | 1.1329e-203 | chr3:169384298-169490555 | 2
11q13.3 | 1.1292e-159 | 4.8338e-119 | chr11:69451838-69502928 | 2
19q12 | 2.1409e-98 | 3.9538e-98 | chr19:30306758-30316875 | 1
17q12 | 1.027e-103 | 1.1306e-79 | chr17:37848534-37876887 | 1
8p11.23 | 6.1757e-87 | 1.9588e-58 | chr8:38170522-38260814 | 2
1q21.3 | 3.6865e-72 | 2.5963e-44 | chr1:150493148-150739128 | 8
4q12 | 9.4376e-38 | 9.4376e-38 | chr4:55139083-55166866 | 1
20q13.2 | 1.0226e-31 | 9.9221e-30 | chr20:52156848-52427475 | 1
1q32.1 | 8.6004e-54 | 5.9546e-26 | chr1:204367383-204548517 | 3
12q14.1 | 2.2382e-44 | 1.2889e-24 | chr12:58125396-58156509 | 5
5p15.33 | 2.4292e-21 | 2.4292e-21 | chr5:1287704-1314315 | 2
19p13.12 | 2.5296e-25 | 9.0266e-20 | chr19:15312574-15416153 | 2
17q25.3 | 1.0474e-30 | 2.3775e-19 | chr17:77760765-77822862 | 3
15q26.3 | 2.2618e-17 | 2.2618e-17 | chr15:98907098-99776125 | 6
11q14.1 | 4.4187e-70 | 8.3997e-15 | chr11:77431241-78030045 | 11
8p11.21 | 1.0694e-48 | 1.6622e-14 | chr8:41746093-42001905 | 2
1p34.2 | 2.5575e-17 | 6.514e-13 | chr1:39688460-40592392 | 17
12p13.33 | 1.6145e-20 | 7.5818e-13 | chr12:1-1078102 | 12
12q15 | 6.1875e-34 | 1.1707e-11 | chr12:69178021-69278368 | 2
6p22.3 | 2.0733e-12 | 4.7977e-09 | chr6:18379939-18698180 | 3
7q36.3 | 9.0786e-08 | 9.0786e-08 | chr7:154958350-159138663 | 26
Xq28 | 3.7725e-07 | 3.7725e-07 | chrX:152916868-154883395 | 76
1p22.3 | 2.4378e-13 | 9.2452e-07 | chr1:85979933-86002734 | 1
1q44 | 8.6305e-33 | 1.4154e-06 | chr1:242974745-245940819 | 17
5q35.3 | 1.7841e-06 | 1.7841e-06 | chr5:176049709-177059713 | 30
13q34 | 2.1663e-06 | 2.1663e-06 | chr13:109713210-111769200 | 11
10q22.3 | 3.6655e-06 | 3.6655e-06 | chr10:79538735-79739599 | 3
20q11.21 | 4.4422e-10 | 4.6015e-06 | chr20:30171851-30326379 | 5
4p16.3 | 0.00073223 | 0.00073223 | chr4:1778797-1817427 | 2
6q21 | 0.00092082 | 0.00094441 | chr6:107198224-107299416 | 2
10p15.1 | 0.0068631 | 0.0068631 | chr10:1-6398978 | 46
2q31.2 | 0.023226 | 0.023226 | chr2:176985697-179121042 | 25
18q11.2 | 0.023687 | 0.023687 | chr18:23801518-24158561 | 2
14q32.33 | 0.058886 | 0.058886 | chr14:105172079-105333748 | 7
19p13.2 | 6.7046e-08 | 0.072981 | chr19:7300056-7398264 | 0 [INSR]
12p12.1 | 7.468e-08 | 0.079878 | chr12:24885718-25925171 | 7
6p21.1 | 0.00060419 | 0.09318 | chr6:43462203-44064063 | 13

Genes in Wide Peak

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

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

Genes
MYC

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 3q26.2.

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

Genes
TERC
ARPM1

Genes in Wide Peak

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

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

Genes
CCND1
ORAOV1

Genes in Wide Peak

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

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

Genes
CCNE1

Genes in Wide Peak

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

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

Genes
ERBB2

Genes in Wide Peak

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

Table S7. 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 1q21.3.

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

Genes
hsa-mir-4257
CTSS
ENSA
MCL1
ADAMTSL4
GOLPH3L
HORMAD1
MIR4257

Genes in Wide Peak

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

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

Genes
PDGFRA

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 20q13.2.

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

Genes
ZNF217

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q32.1.

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

Genes
MDM4
PIK3C2B
PPP1R15B

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12q14.1.

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

Genes
CDK4
CYP27B1
TSPAN31
MARCH9
AGAP2

Genes in Wide Peak

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

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

Genes
TERT
MIR4457

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19p13.12.

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

Genes
BRD4
EPHX3

Genes in Wide Peak

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

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

Genes
CBX4
CBX8
CBX2

Genes in Wide Peak

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

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

Genes
IGF1R
SYNM
TTC23
PGPEP1L
FAM169B
MIR4714

Genes in Wide Peak

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

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

Genes
NDUFC2
THRSP
GAB2
C11orf67
RSF1
USP35
KCTD14
ALG8
INTS4
KCTD21
NDUFC2-KCTD14

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 8p11.21.

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

Genes
ANK1
KAT6A

Genes in Wide Peak

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

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

Genes
MYCL1
BMP8B
PPT1
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 12p13.33.

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

Genes
KDM5A
NINJ2
RAD52
SLC6A12
SLC6A13
WNK1
CCDC77
B4GALNT3
IQSEC3
LOC574538
FAM138D
LOC100288778

Genes in Wide Peak

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

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

Genes
MDM2
CPM

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p22.3.

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

Genes
hsa-mir-548a-1
RNF144B
MIR548A1

Genes in Wide Peak

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

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

Genes
hsa-mir-595
hsa-mir-153-2
EN2
MNX1
INSIG1
PTPRN2
SHH
VIPR2
UBE3C
DNAJB6
NCAPG2
WDR60
ESYT2
LMBR1
LINC00244
NOM1
C7orf13
RNF32
LOC154822
RBM33
CNPY1
LOC285889
MIR153-2
LOC645249
MIR595
LOC100506585

Genes in Wide Peak

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

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

Genes
MTCP1
hsa-mir-1184-3
hsa-mir-1184-2
hsa-mir-1184-1
hsa-mir-718
ABCD1
ARHGAP4
ATP6AP1
AVPR2
CLIC2
CTAG1B
TEX28
DKC1
DNASE1L1
EMD
F8
FLNA
G6PD
OPN1MW
GDI1
HCFC1
IDH3G
IRAK1
L1CAM
MECP2
MPP1
PLXNB3
OPN1LW
RENBP
RPL10
SLC6A8
SSR4
TAZ
VBP1
NAA10
F8A1
UBL4A
TMEM187
LAGE3
SLC10A3
TKTL1
IKBKG
FAM50A
BCAP31
SRPK3
SNORA70
CTAG2
TMLHE
PLXNA3
PDZD4
FAM3A
FUNDC2
BRCC3
H2AFB3
RAB39B
GAB3
PNCK
CTAG1A
LINC00204B
H2AFB2
H2AFB1
F8A2
F8A3
SNORA36A
SNORA56
OPN1MW2
CXorf68
LINC00204A
MTCP1NB
MIR1184-1
MIR718
MIR3202-2
MIR1184-3
MIR1184-2
MIR3202-1
LOC100507404

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1p22.3.

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

Genes
DDAH1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q44.

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

Genes
ADSS
HNRNPU
CEP170
AKT3
ZNF238
SDCCAG8
PPPDE1
KIF26B
SMYD3
EFCAB2
FAM36A
C1orf100
C1orf101
HNRNPU-AS1
LOC339529
LOC731275
MIR4677

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 5q35.3.

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

Genes
NSD1
hsa-mir-4281
DBN1
F12
FGFR4
GRK6
HK3
SLC34A1
SNCB
PDLIM7
RGS14
LMAN2
B4GALT7
ZNF346
TSPAN17
PRELID1
DDX41
UIMC1
RAB24
FAM193B
TMED9
DOK3
PRR7
MXD3
UNC5A
LOC202181
EIF4E1B
LOC340037
PFN3
MIR4281

Genes in Wide Peak

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

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

Genes
COL4A1
COL4A2
ING1
IRS2
ARHGEF7
MYO16
ANKRD10
RAB20
CARKD
CARS2
LINC00346

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q22.3.

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

Genes
DLG5
POLR3A
LOC100128292

Genes in Wide Peak

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

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

Genes
hsa-mir-3193
BCL2L1
ID1
COX4I2
MIR3193

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4p16.3.

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

Genes
FGFR3
LETM1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6q21.

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

Genes
hsa-mir-587
LOC100422737

Genes in Wide Peak

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

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

Genes
hsa-mir-3155
ADARB2
CALML3
AKR1C4
KLF6
AKR1C1
AKR1C2
GDI2
IDI1
IL2RA
IL15RA
PFKFB3
PFKP
AKR1C3
NET1
PITRM1
ZMYND11
WDR37
DIP2C
LARP4B
GTPBP4
CALML5
ANKRD16
FAM208B
IDI2-AS1
ASB13
TUBAL3
AKR1E2
FBXO18
RBM17
IDI2
UCN3
LOC282980
LOC338588
AKR1CL1
TUBB8
tAKR
LINC00200
LOC399708
LOC399715
C10orf108
ADARB2-AS1
LOC100216001
MIR3155A
LOC100507034
MIR3155B

Genes in Wide Peak

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

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

Genes
NFE2L2
hsa-mir-3128
hsa-mir-1246
hsa-mir-10b
HOXD1
HOXD3
HOXD4
HOXD8
HOXD9
AGPS
MTX2
PDE11A
TTC30A
OSBPL6
RBM45
TTC30B
HNRNPA3
LOC375295
LOC401022
MIR10B
LOC100130691
MIR1246
MIR3128
LOC100506783
MIR4444-1

Genes in Wide Peak

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

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

Genes
TAF4B
KCTD1

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q32.33.

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

Genes
AKT1
SIVA1
INF2
ADSSL1
MGC23270
KIAA0284
ZBTB42

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 12p12.1.

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

Genes
KRAS
BCAT1
LRMP
CASC1
LYRM5
IFLTD1
C12orf77

Genes in Wide Peak

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

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

Genes
POLH
VEGFA
POLR1C
MAD2L1BP
YIPF3
GTPBP2
MRPS18A
XPO5
TJAP1
C6orf223
RSPH9
LRRC73
LOC100132354

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 | 0 | 0 | chr9:21800514-22448737 | 5
19p13.3 | 1.79e-184 | 1.79e-184 | chr19:1427261-1882761 | 18
8p23.2 | 8.5653e-148 | 1.3483e-119 | chr8:2079140-6262191 | 1
5q11.2 | 2.178e-129 | 9.5808e-110 | chr5:58145167-59787985 | 3
10q23.31 | 6.1714e-127 | 1.1551e-107 | chr10:89615138-90034038 | 2
6q26 | 7.7586e-117 | 2.8938e-96 | chr6:161693099-163153207 | 1
13q14.2 | 1.6202e-105 | 1.2892e-88 | chr13:48833767-49064807 | 2
4q34.3 | 1.6011e-102 | 6.5353e-78 | chr4:178911874-183060693 | 1
22q13.31 | 1.0702e-66 | 1.0702e-66 | chr22:47571204-48018269 | 1
11p15.5 | 1.0161e-63 | 1.0161e-63 | chr11:1-748945 | 36
16q23.1 | 2.1963e-61 | 2.1963e-61 | chr16:78129058-79627770 | 1
16p13.3 | 6.1781e-47 | 6.4134e-47 | chr16:5144019-7771745 | 1
1p36.11 | 8.9861e-113 | 4.7443e-44 | chr1:26900639-27191410 | 4
1p36.23 | 7.5563e-122 | 1.1698e-40 | chr1:7829287-8423509 | 7
3p14.2 | 3.7337e-53 | 2.8945e-40 | chr3:59034763-61547330 | 1
2q22.1 | 7.9458e-42 | 7.9216e-32 | chr2:139655617-143637838 | 1
15q15.1 | 6.9377e-57 | 8.8889e-30 | chr15:41795901-42121792 | 6
17q11.2 | 1.613e-29 | 2.7313e-29 | chr17:29326736-29722618 | 5
4q22.1 | 1.912e-44 | 4.5304e-29 | chr4:90844993-93240505 | 1
11q25 | 3.0279e-27 | 3.0525e-27 | chr11:133400280-135006516 | 14
18q23 | 1.0436e-46 | 8.8761e-24 | chr18:74678491-78077248 | 14
2q37.3 | 1.1136e-36 | 1.9048e-22 | chr2:240983601-243199373 | 40
14q24.1 | 3.0444e-17 | 2.9783e-17 | chr14:68275375-69288431 | 2
7p22.3 | 7.889e-17 | 7.889e-17 | chr7:1-1303032 | 19
20p12.1 | 7.3377e-16 | 7.3377e-16 | chr20:14302876-16036135 | 3
17p12 | 1.5051e-15 | 2.6569e-15 | chr17:11896630-12456081 | 3
Xp21.2 | 2.8862e-13 | 2.8862e-13 | chrX:30865118-34644819 | 4
10q26.3 | 2.5825e-32 | 5.1457e-10 | chr10:135190263-135214343 | 1
21q11.2 | 2.067e-09 | 2.067e-09 | chr21:1-15482604 | 16
3p26.3 | 1.2397e-17 | 4.2893e-09 | chr3:1-4396118 | 8
6p25.3 | 8.7321e-09 | 8.5699e-09 | chr6:1608837-2252425 | 2
19q13.32 | 9.347e-27 | 8.7908e-09 | chr19:47136847-47908503 | 25
8p21.2 | 1.0948e-69 | 1.5213e-08 | chr8:22785402-26374565 | 30
18q21.2 | 7.2927e-24 | 2.3254e-05 | chr18:48514396-48705371 | 1
12q24.33 | 6.3143e-14 | 0.00012827 | chr12:131692956-133851895 | 27
5q21.3 | 8.5632e-34 | 0.00021028 | chr5:96474254-118175941 | 59
19q13.43 | 8.166e-24 | 0.000486 | chr19:58457932-59128983 | 31
9q34.3 | 9.5631e-05 | 0.00065322 | chr9:132797579-139390249 | 107
10p15.3 | 0.0032252 | 0.0032106 | chr10:1-699088 | 3
15q11.2 | 7.8828e-32 | 0.00585 | chr15:1-31198928 | 157
6q22.31 | 3.8962e-19 | 0.0062362 | chr6:123955968-125232805 | 1
7q36.1 | 0.0068963 | 0.0068963 | chr7:151817415-152136074 | 1
12q23.1 | 4.4619e-12 | 0.009494 | chr12:99124001-100431272 | 2
12p13.1 | 0.018307 | 0.018153 | chr12:12710990-13031888 | 8
9p24.1 | 3.1236e-29 | 0.028854 | chr9:7799607-12693402 | 1
4p16.3 | 0.04328 | 0.043184 | chr4:1-1284820 | 28
9p13.1 | 1.1328e-08 | 0.10351 | chr9:38619152-71152237 | 50
13q11 | 2.1704e-16 | 0.11273 | chr13:1-20535070 | 10
1p13.2 | 5.8293e-07 | 0.13189 | chr1:79128619-119913683 | 283
2p25.3 | 0.13606 | 0.13606 | chr2:1-16089614 | 77

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
MTAP
C9orf53
CDKN2B-AS1

Genes in Wide Peak

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

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

Genes
TCF3
hsa-mir-1909
RPS15
APC2
UQCR11
MBD3
PCSK4
REXO1
KLF16
REEP6
PLK5
C19orf25
ATP8B3
ADAMTSL5
ONECUT3
MEX3D
LOC100288123
MIR1909

Genes in Wide Peak

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

Table S41. 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 5q11.2.

Table S42. 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 10q23.31.

Table S43. 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 6q26.

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

Genes
PARK2

Genes in Wide Peak

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

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

Genes
RB1
LPAR6

Genes in Wide Peak

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

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

Genes
LINC00290

Genes in Wide Peak

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

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

Genes
LOC339685

Genes in Wide Peak

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

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

Genes
HRAS
hsa-mir-210
DRD4
IRF7
PSMD13
RNH1
SCT
RASSF7
IFITM1
IFITM3
DEAF1
IFITM2
PKP3
SIRT3
BET1L
CDHR5
PHRF1
SIGIRR
RIC8A
EPS8L2
ATHL1
PTDSS2
ODF3
LRRC56
LOC143666
SCGB1C1
NLRP6
C11orf35
TMEM80
ANO9
B4GALNT4
IFITM5
MIR210
LOC653486
LOC100133161
MIR210HG

Genes in Wide Peak

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

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

Genes
WWOX

Genes in Wide Peak

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

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

Genes
RBFOX1

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 1p36.11.

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

Genes
ARID1A
SFN
PIGV
ZDHHC18

Genes in Wide Peak

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

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

Genes
TNFRSF9
PER3
VAMP3
UTS2
PARK7
SLC45A1
ERRFI1

Genes in Wide Peak

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

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

Genes
FHIT

Genes in Wide Peak

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

Table S54. 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 15q15.1.

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

Genes
hsa-mir-626
TYRO3
MAPKBP1
MGA
RPAP1
MIR626

Genes in Wide Peak

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

Table S56. 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 4q22.1.

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

Genes
FAM190A

Genes in Wide Peak

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

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

Genes
IGSF9B
NCAPD3
ACAD8
B3GAT1
THYN1
JAM3
GLB1L2
VPS26B
GLB1L3
SPATA19
LOC283174
LOC283177
LOC100128239
MIR4697

Genes in Wide Peak

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

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

Genes
GALR1
MBP
NFATC1
CTDP1
TXNL4A
ADNP2
KCNG2
SALL3
RBFA
PQLC1
PARD6G
ATP9B
HSBP1L1
LOC100130522

Genes in Wide Peak

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

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

Genes
hsa-mir-3133
hsa-mir-149
AGXT
KIF1A
BOK
DTYMK
GPC1
GPR35
HDLBP
SEPT2
PDCD1
PPP1R7
FARP2
STK25
CAPN10
PASK
ATG4B
SNED1
ANO7
THAP4
ANKMY1
RNPEPL1
GAL3ST2
C2orf54
ING5
NEU4
MTERFD2
OTOS
MYEOV2
OR6B3
LOC200772
CXXC11
DUSP28
AQP12A
MIR149
AQP12B
D2HGDH
LOC728323
PP14571
BOK-AS1

Genes in Wide Peak

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

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

Genes
ZFP36L1
RAD51B

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 7p22.3.

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

Genes
hsa-mir-339
GPER
PDGFA
PRKAR1B
ADAP1
SUN1
GET4
CYP2W1
HEATR2
FAM20C
C7orf50
ZFAND2A
COX19
GPR146
UNCX
FLJ44511
LOC442497
MIR339
LOC100288524

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20p12.1.

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

Genes
FLRT3
MACROD2
MACROD2-AS1

Genes in Wide Peak

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

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

Genes
MAP2K4
hsa-mir-744
MIR744

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for Xp21.2.

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

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

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 10q26.3.

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

Genes
PAOX

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 21q11.2.

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

Genes
hsa-mir-3118-5
hsa-mir-3156-3
BAGE
TPTE
C21orf15
BAGE5
BAGE4
BAGE3
BAGE2
ANKRD30BP2
POTED
ANKRD20A11P
TEKT4P2
MIR3156-3
MIR3687
MIR3648

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p26.3.

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

Genes
IL5RA
SETMAR
CHL1
CNTN6
TRNT1
CRBN
LRRN1
CNTN4

Genes in Wide Peak

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

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

Genes
FOXC1
GMDS

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 19q13.32.

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

Genes
hsa-mir-3191
hsa-mir-320e
C5AR1
AP2S1
ARHGAP35
NPAS1
SLC1A5
DHX34
SAE1
ZC3H4
PRKD2
CCDC9
BBC3
GPR77
STRN4
TMEM160
FKRP
GNG8
DACT3
PRR24
SNAR-E
MIR3191
MIR3190
MIR320E
LOC100506068

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 8p21.2.

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

Genes
BNIP3L
GNRH1
LOXL2
NEFM
NEFL
NKX3-1
PPP2R2A
STC1
ADAM7
TNFRSF10D
TNFRSF10C
TNFRSF10B
TNFRSF10A
ENTPD4
PNMA2
ADAM28
RHOBTB2
ADAMDEC1
SLC25A37
KCTD9
EBF2
DOCK5
CHMP7
NKX2-6
CDCA2
R3HCC1
LOC254896
LOC286059
LOC389641
LOC100507156

Genes in Wide Peak

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

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

Genes
SMAD4

Genes in Wide Peak

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

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

Genes
GOLGA3
MMP17
POLE
PXMP2
SFSWAP
ZNF10
ZNF26
ZNF84
ZNF140
ULK1
ZNF268
P2RX2
ANKLE2
GALNT9
CHFR
EP400
FBRSL1
NOC4L
PUS1
PGAM5
DDX51
EP400NL
LOC647589
SNORA49
LOC100130238
ZNF605
LOC100507055

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 5q21.3.

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

Genes
APC
hsa-mir-548f-3
hsa-mir-548p
CAMK4
CDO1
CHD1
AP3S1
EFNA5
FER
KCNN2
MAN2A1
MCC
PAM
PGGT1B
SRP19
ST8SIA4
REEP5
ATG12
NREP
RAB9BP1
PJA2
PPIP5K2
TMED7
COMMD10
FLJ11235
GIN1
TRIM36
RIOK2
FEM1C
SEMA6A
EPB41L4A
FBXL17
YTHDC2
NUDT12
TSSK1B
TSLP
C5orf30
SLC25A46
EPB41L4A-AS1
SLCO6A1
STARD4
WDR36
CCDC112
DCP2
AQPEP
RGMB
FAM174A
SLCO4C1
TICAM2
FLJ35946
TMEM232
LOC644100
SNORA13
LOC728342
LOC100133050
LOC100289230
LOC100289673
TMED7-TICAM2
LOC100505678

Genes in Wide Peak

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

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

Genes
A1BG
RPS5
ZNF8
MZF1
ZNF132
ZNF135
UBE2M
TRIM28
ZNF274
SLC27A5
ZNF324
CHMP2A
ZNF544
ZNF446
ZSCAN18
MGC2752
ZNF329
ZNF606
ZBTB45
ZNF837
C19orf18
ZNF497
ZNF584
ZSCAN1
ZSCAN22
ZNF324B
A1BG-AS1
LOC646862
LOC100128398
LOC100131691
MIR4754

Genes in Wide Peak

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

Table S76. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ABL1
RALGDS
TSC1
BRD3
NUP214
ABO
ASS1
CEL
CELP
COL5A1
DBH
SARDH
FCN1
FCN2
RAPGEF1
LCN1
PAEP
RPL7A
RXRA
SNAPC4
SURF1
SURF2
SURF4
MED22
SURF6
TTF1
VAV2
LHX3
GFI1B
FUBP3
GTF3C5
GTF3C4
MED27
ADAMTSL2
PPP1R26
SEC16A
LAMC3
UBAC1
OLFM1
POMT1
SDCCAG3
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
SETX
PMPCA
EXOSC2
NCS1
GPSM1
DKFZP434A062
GBGT1
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
OBP2B
OBP2A
MRPS2
INPP5E
BARHL1
REXO4
KCNT1
GPR107
PRDM12
CARD9
DDX31
AIF1L
UCK1
NTNG2
PRRC2B
PPAPDC3
FIBCD1
C9orf69
NACC2
C9orf116
CAMSAP1
C9orf163
AK8
C9orf96
QSOX2
LINC00094
FAM78A
QRFP
GLT6D1
C9orf171
TMEM8C
LCN9
LOC401557
SOHLH1
FAM163B
SNORD62B
DNLZ
LOC100130954
RNU6ATAC
LOC100272217
MIR3689A
MIR3689B
LOC100506599
MIR3689D1
MIR3689F
MIR4669
MIR3689C
MIR3689D2
MIR3689E

Genes in Wide Peak

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

Table S77. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ZMYND11
TUBB8
C10orf108

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q11.2.

Table S78. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-1268
hsa-mir-3118-6
hsa-mir-3118-4
APBA2
NBEAP1
GABRA5
GABRB3
GABRG3
IPW
NDN
OCA2
SNRPN
TJP1
UBE3A
MKRN3
PAR5
HERC2
SNURF
CYFIP1
FAM189A1
C15orf2
DKFZP434L187
MAGEL2
NDNL2
ATP10A
NIPA2
CHRFAM7A
ULK4P3
ULK4P1
ARHGAP11B
SNORD107
TUBGCP5
NIPA1
PAR1
LOC283683
OR4N4
HERC2P3
GOLGA6L1
GOLGA8G
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
SNORD64
PAR4
PAR-SN
LOC348120
GOLGA8E
OR4M2
OR4N3P
HERC2P2
NF1P2
HERC2P9
WHAMMP2
LOC503519
CHEK2P2
LOC646214
CXADRP2
LOC646278
REREP3
LOC653061
LOC653075
SNORD116-19
GOLGA6L6
LOC727924
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
HERC2P7
GOLGA8F
GOLGA8DP
ULK4P2
LOC100288637
LOC100289656
MIR4509-1
MIR4509-2
MIR4508
MIR4509-3
MIR4715

Genes in Wide Peak

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

Table S79. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
NKAIN2

Genes in Wide Peak

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

Table S80. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
MLL3

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q23.1.

Table S81. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ANKS1B
FAM71C

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12p13.1.

Table S82. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-613
CDKN1B
CREBL2
GPR19
DDX47
APOLD1
RPL13AP20
MIR613

Genes in Wide Peak

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

Table S83. 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 4p16.3.

Table S84. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-571
ATP5I
CTBP1
DGKQ
GAK
IDUA
MYL5
PDE6B
ZNF141
PCGF3
SPON2
CPLX1
SLC26A1
FGFRL1
PIGG
ABCA11P
MFSD7
TMEM175
C4orf42
ZNF595
ZNF721
ZNF718
RNF212
ZNF876P
ZNF732
LOC100129917
LOC100130872
TMED11P

Genes in Wide Peak

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

Table S85. 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 13q11.

Table S86. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
TUBA3C
ZMYM5
MPHOSPH8
PSPC1
TPTE2
PHF2P1
ANKRD20A9P
LINC00442
ANKRD26P3
LINC00421

Genes in Wide Peak

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

Table S87. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
NRAS
BCL10
TRIM33
RBM15
hsa-mir-942
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
hsa-mir-553
hsa-mir-137
hsa-mir-760
ABCA4
ADORA3
AGL
ALX3
AMPD1
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
ATP1A1
ATP5F1
BRDT
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CLCA1
CNN3
COL11A1
CSF1
CTBS
DBT
DPYD
DR1
S1PR1
CELSR2
EXTL2
F3
GBP1
GBP2
GBP3
GFI1
GCLM
GNAI3
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
IGSF3
CYR61
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
PRKACB
PKN2
PSMA5
PTGFRN
ABCD3
RAP1A
SNORD21
RPL5
SORT1
SARS
SLC16A1
STXBP3
SYCP1
TAF13
TBX15
TGFBR3
TSHB
VCAM1
WNT2B
CSDE1
EVI5
CDC7
BCAR3
TTF2
LMO4
CDC14A
RTCD1
SLC16A4
CD101
SEP15
ARHGAP29
CLCA3P
CLCA2
HS2ST1
LRIG2
LPPR4
TSPAN2
BCAS2
WARS2
CEPT1
VAV3
HBXIP
AP4B1
PHTF1
AHCYL1
WDR3
MAN1A2
GLMN
DDX20
CLCA4
MTF2
NTNG1
WDR47
CLCC1
LPHN2
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
RWDD3
PTPN22
SNORA66
CHIA
GPSM2
SLC25A24
DNTTIP2
TMED5
SH3GLB1
SNX7
DPH5
GPR88
CCDC76
RSBN1
ZNHIT6
GDAP2
FAM46C
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
MCOLN3
SLC22A15
RNPC3
LRIF1
CTTNBP2NL
FAM212B
CCBL2
TMEM167B
OLFML3
AMIGO1
ODF2L
KIAA1324
PTBP2
DNASE2B
ELTD1
HIAT1
DCLRE1B
WDR77
EPS8L3
VTCN1
TTLL7
RPAP2
DENND2D
RPF1
SIKE1
TRIM45
VANGL1
GPR61
SYDE2
ZNF644
LRRC8C
PROK1
PSRC1
ATP1A1OS
FAM40A
DNAJA1P5
HENMT1
GBP4
GBP5
SSX2IP
OLFM3
WDR63
MAB21L3
SLC44A3
ATXN7L2
C1orf194
LRRC39
DRAM2
C1orf88
C1orf162
SYT6
SAMD13
C1orf52
TMEM56
NBPF4
SLC30A7
RP11-165H20.1
DENND2C
GBP6
LPPR5
FNDC7
SASS6
HFM1
UBL4B
ALG14
SPAG17
HIPK1
AKR7A2P1
EPHX4
AKNAD1
MCOLN2
COL24A1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
ZNF326
BTBD8
PPM1J
LOC339524
CCDC18
MYBPHL
BARHL2
HSP90B3P
GBP7
C1orf146
FAM69A
SLC6A17
UOX
FRRS1
GBP1P1
FLJ27354
MIR137HG
MIR137
MIR197
C1orf180
FLJ31662
LOC440600
BCL2L15
PGCP1
GEMIN8P4
RBMXL1
SRG7
CYMP
LOC643441
LOC646626
LOC648740
NBPF6
SCARNA2
MIR548D1
MIR553
LOC729970
LOC729987
MIR942
MIR760
LOC100128787
LOC100129046
LOC100129138
LOC100129269
LOC100129620
LOC100131564
LOC100287722
MIR320B1
MIR4256
MIR548AA1
LOC100505768
LOC100506343
TMEM56-RWDD3
MIR2682
MIR4423

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 2p25.3.

Table S88. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
MYCN
hsa-mir-3125
hsa-mir-4262
hsa-mir-548s
hsa-mir-4261
ACP1
DDX1
E2F6
HPCAL1
ID2
KCNF1
ODC1
RPS7
RRM2
SOX11
ADAM17
TPO
TSSC1
PXDN
KLF11
ASAP2
TAF1B
ITGB1BP1
ROCK2
GREB1
RNF144A
PDIA6
MYCNOS
YWHAQ
MYT1L
LPIN1
NTSR2
SH3YL1
TRIB2
GRHL1
TRAPPC12
NBAS
CPSF3
SNTG2
ADI1
ALLC
KIDINS220
COLEC11
NOL10
RSAD2
CMPK2
MBOAT2
TMEM18
C2orf50
PQLC3
LOC150622
FAM84A
CYS1
ATP6V1C2
RNASEH1
FAM150B
IAH1
FLJ33534
LOC339788
LINC00299
LOC339822
C2orf48
LOC386597
LOC400940
LINC00487
FAM110C
LOC727982
LOC730811
SNORA80B
MIR4261
MIR3125
MIR4262
LOC100505964
LOC100506054
LOC100506274
LOC100506474
MIR4429

Arm-level results

Table 3. Get Full Table Arm-level significance table - 32 significant results found.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.15 | -3.29 | 1 | 0.19 | 2.42 | 0.0136
1q | 1955 | 0.33 | 23.6 | 0 | 0.14 | -4.9 | 1
2p | 924 | 0.19 | -5.4 | 1 | 0.09 | -17.5 | 1
2q | 1556 | 0.15 | -6.6 | 1 | 0.10 | -13.7 | 1
3p | 1062 | 0.15 | -8.46 | 1 | 0.30 | 10.7 | 0
3q | 1139 | 0.24 | 3.03 | 0.00615 | 0.16 | -7.92 | 1
4p | 489 | 0.07 | -20.9 | 1 | 0.31 | 9.56 | 0
4q | 1049 | 0.06 | -19.8 | 1 | 0.30 | 12.1 | 0
5p | 270 | 0.26 | 0.816 | 0.829 | 0.19 | -7.83 | 1
5q | 1427 | 0.17 | -4.49 | 1 | 0.25 | 6.61 | 4.13e-11
6p | 1173 | 0.17 | -5.29 | 1 | 0.20 | -1.51 | 1
6q | 839 | 0.14 | -11.2 | 1 | 0.26 | 4.23 | 2.21e-05
7p | 641 | 0.43 | 26.9 | 0 | 0.14 | -11.1 | 1
7q | 1277 | 0.41 | 29.9 | 0 | 0.12 | -11 | 1
8p | 580 | 0.22 | -1.8 | 1 | 0.43 | 24.9 | 0
8q | 859 | 0.37 | 19 | 0 | 0.17 | -6.99 | 1
9p | 422 | 0.15 | -11.5 | 1 | 0.36 | 14.7 | 0
9q | 1113 | 0.13 | -11.2 | 1 | 0.31 | 13.4 | 0
10p | 409 | 0.19 | -7.43 | 1 | 0.32 | 9.19 | 0
10q | 1268 | 0.12 | -10.9 | 1 | 0.33 | 16.7 | 0
11p | 862 | 0.11 | -15.5 | 1 | 0.22 | -1.4 | 1
11q | 1515 | 0.11 | -11.7 | 1 | 0.22 | 3.9 | 8.74e-05
12p | 575 | 0.25 | 1.89 | 0.13 | 0.14 | -12.8 | 1
12q | 1447 | 0.20 | -0.0532 | 1 | 0.12 | -10.6 | 1
13q | 654 | 0.21 | -3.52 | 1 | 0.36 | 15.7 | 0
14q | 1341 | 0.13 | -10.2 | 1 | 0.32 | 15.8 | 0
15q | 1355 | 0.09 | -15.3 | 1 | 0.28 | 11.6 | 0
16p | 872 | 0.22 | -1.49 | 1 | 0.26 | 4.39 | 1.15e-05
16q | 702 | 0.16 | -8.92 | 1 | 0.36 | 17.8 | 0
17p | 683 | 0.09 | -16.1 | 1 | 0.46 | 32.3 | 0
17q | 1592 | 0.16 | -4.32 | 1 | 0.27 | 10.7 | 0
18p | 143 | 0.17 | -10.5 | 1 | 0.35 | 11.1 | 0
18q | 446 | 0.14 | -12.4 | 1 | 0.36 | 15.5 | 0
19p | 995 | 0.23 | 0.462 | 1 | 0.19 | -3.6 | 1
19q | 1709 | 0.23 | 5.79 | 1.96e-08 | 0.18 | -1.79 | 1
20p | 355 | 0.41 | 21.9 | 0 | 0.13 | -13 | 1
20q | 753 | 0.45 | 30.4 | 0 | 0.09 | -16.1 | 1
21q | 509 | 0.15 | -11.5 | 1 | 0.24 | -0.404 | 1
22q | 921 | 0.14 | -10.1 | 1 | 0.38 | 22.2 | 0
Xq | 1312 | 0.15 | -7.59 | 1 | 0.25 | 6.68 | 2.68e-11

Methods & Data
Input
Description

- Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

- Markers File: The markers file identifies the marker names and positions of the markers in the original dataset (before segmentation). It is a three column, tab-delimited file with an optional header. The column headers are: (1) Marker Name, (2) Chromosome, (3) Marker Position (in bases).

- Reference Genome: The reference genome file contains information about the location of genes and cytobands on a given build of the genome. Reference genome files are created in Matlab and are not viewable with a text editor.

- CNV Files: There are two options for the cnv file. The first option allows CNVs to be identified by marker name. The second option allows the CNVs to be identified by genomic location. Option #1: A two column, tab-delimited file with an optional header row. The marker names given in this file must match the marker names given in the markers file. The CNV identifiers are for user use and can be arbitrary. The column headers are: (1) Marker Name, (2) CNV Identifier. Option #2: A 6 column, tab-delimited file with an optional header row. The 'CNV Identifier' is for user use and can be arbitrary. 'Narrow Region Start' and 'Narrow Region End' are also not used. The column headers are: (1) CNV Identifier, (2) Chromosome, (3) Narrow Region Start, (4) Narrow Region End, (5) Wide Region Start, (6) Wide Region End

- Amplification Threshold: Threshold for copy number amplifications. Regions with a log2 ratio above this value are considered amplified.

- Deletion Threshold: Threshold for copy number deletions. Regions with a log2 ratio below the negative of this value are considered deletions.

- Cap Values: Minimum and maximum cap values on analyzed data. Regions with a log2 ratio greater than the cap are set to the cap value; regions with a log2 ratio less than -cap value are set to -cap. Values must be positive.

- Broad Length Cutoff: Threshold used to distinguish broad from focal events, given in units of fraction of chromosome arm.

- Remove X-Chromosome: Flag indicating whether to remove data from the X-chromosome before analysis. Allowed values= {1,0} (1: Remove X-Chromosome, 0: Do not remove X-Chromosome.

- Confidence Level: Confidence level used to calculate the region containing a driver.

- Join Segment Size: Smallest number of markers to allow in segments from the segmented data. Segments that contain fewer than this number of markers are joined to the neighboring segment that is closest in copy number.

- Arm Level Peel Off: Flag set to enable arm-level peel-off of events during peak definition. The arm-level peel-off enhancement to the arbitrated peel-off method assigns all events in the same chromosome arm of the same sample to a single peak. It is useful when peaks are split by noise or chromothripsis. Allowed values= {1,0} (1: Use arm level peel off, 0: Use normal arbitrated peel-off).

- Maximum Sample Segments: Maximum number of segments allowed for a sample in the input data. Samples with more segments than this threshold are excluded from the analysis.

Values

List of inputs used for this run of GISTIC2. All files listed should be included in the archived results.

- Segmentation File = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/PANCAN8/1764788/2.GDAC_MergeDataFiles.Finished/PANCAN8.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt

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

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

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

- Amplification Threshold = 0.1

- Deletion Threshold = 0.1

- Cap Values = 1.5

- Broad Length Cutoff = 0.7

- Remove X-Chromosome = 0

- Confidence Level = 0.99

- Join Segment Size = 4

- Arm Level Peel Off = 1

- Maximum Sample Segments = 2000

Table 4. Get Full Table First 10 out of 3770 Input Tumor Samples.

Tumor Sample Names
TCGA-02-0001-01C-01D-0182-01
TCGA-02-0003-01A-01D-0182-01
TCGA-02-0006-01B-01D-0182-01
TCGA-02-0007-01A-01D-0182-01
TCGA-02-0009-01A-01D-0182-01
TCGA-02-0010-01A-01D-0182-01
TCGA-02-0011-01B-01D-0182-01
TCGA-02-0014-01A-01D-0182-01
TCGA-02-0015-01A-01G-0293-01
TCGA-02-0016-01A-01G-0293-01

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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