Copy number analysis (GISTIC2)
PANCANCER cohort with 12 disease types (Primary solid tumor)
21 April 2013 | analyses__2013_04_21
Maintainer Information
Citation Information
doi:10.7908/C1736NW2
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): PANCANCER cohort with 12 disease types (Primary solid tumor cohort) - 21 April 2013: Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C1736NW2
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 2.0.17a (Firehose task version: 0.0.8).

Summary

There were 4976 tumor samples used in this analysis: 33 significant arm-level results, 41 significant focal amplifications, and 51 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 - 41 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 | 0 | 0 | chr8:128739772-128766079 | 1
11q13.3 | 0 | 0 | chr11:69956232-70027203 | 1
7p11.2 | 9.6058e-283 | 8.3115e-282 | chr7:55063359-55095549 | 1
3q26.2 | 5.4886e-264 | 5.4886e-264 | chr3:169396071-169490555 | 2
19q12 | 2.1599e-124 | 5.1192e-124 | chr19:30306758-30316875 | 1
17q12 | 1.2383e-128 | 1.3555e-99 | chr17:37848534-37876018 | 1
8p11.23 | 9.7943e-124 | 3.2468e-86 | chr8:38170522-38237581 | 1
1q21.3 | 8.1283e-112 | 2.2836e-77 | chr1:150496857-150706805 | 8
5p15.33 | 5.7911e-46 | 5.7911e-46 | chr5:1287704-1300024 | 1
4q12 | 3.3468e-37 | 3.3468e-37 | chr4:55159545-55165966 | 1
12q15 | 1.605e-65 | 1.5063e-36 | chr12:69212011-69265277 | 2
20q13.2 | 2.9726e-37 | 3.1221e-34 | chr20:52162398-52427475 | 1
17q25.3 | 5.9268e-35 | 2.8951e-22 | chr17:77770063-77819819 | 2
1q32.1 | 1.8391e-53 | 1.8269e-19 | chr1:204367383-204548517 | 3
8p11.21 | 6.2107e-64 | 1.2529e-17 | chr8:41744095-42008185 | 2
6p22.3 | 8.0483e-23 | 1.34e-17 | chr6:20398838-20535695 | 2
12q14.1 | 4.1313e-45 | 2.5685e-17 | chr12:58135797-58162738 | 6
15q26.3 | 6.0484e-16 | 6.0484e-16 | chr15:98907098-99808556 | 7
1p34.2 | 7.5186e-21 | 1.5187e-15 | chr1:39898645-40546624 | 16
19p13.12 | 2.9551e-21 | 1.7252e-15 | chr19:15310246-15422141 | 3
12p13.33 | 5.5962e-22 | 2.2926e-12 | chr12:1-1064527 | 12
14q13.3 | 6.508e-12 | 6.508e-12 | chr14:36625634-37208255 | 6
Xq28 | 1.5032e-11 | 1.5032e-11 | chrX:153005750-153376406 | 19
20q11.21 | 2.5715e-18 | 4.3812e-11 | chr20:30171851-30320705 | 5
1p22.3 | 4.6377e-18 | 8.4309e-10 | chr1:85979933-86002734 | 1
13q34 | 4.5658e-09 | 4.5658e-09 | chr13:109724719-111776288 | 11
2q31.2 | 1.2215e-05 | 1.2215e-05 | chr2:178072322-178171101 | 6
12p12.1 | 1.0924e-13 | 4.7568e-05 | chr12:25321084-25370699 | 3
4p16.3 | 0.00011724 | 0.00011724 | chr4:1778797-1817427 | 2
5q35.3 | 0.00018388 | 0.00018388 | chr5:176049709-177060263 | 30
1q44 | 1.0543e-34 | 0.00021371 | chr1:242608515-249250621 | 85
10p15.1 | 0.00022408 | 0.00022408 | chr10:5013075-5113710 | 3
10q22.2 | 0.00045507 | 0.00045507 | chr10:76555789-77201107 | 9
18q11.2 | 0.00094597 | 0.00094597 | chr18:23814165-24158561 | 2
9p13.3 | 0.0076903 | 0.0076903 | chr9:35652385-35767752 | 10
7q36.3 | 2.5864e-05 | 0.0116 | chr7:154494617-159138663 | 32
6q21 | 0.038754 | 0.03941 | chr6:107206856-107290700 | 2
19p13.2 | 2.7434e-08 | 0.04249 | chr19:7300056-7398264 | 0 [INSR]
6p21.1 | 0.00041892 | 0.081867 | chr6:43330795-44110798 | 18
2p15 | 0.11134 | 0.11134 | chr2:59851417-63298149 | 22
7q21.2 | 0.0015832 | 0.21529 | chr7:92196092-92530348 | 3

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 11q13.3.

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

Genes
ANO1

Genes in Wide Peak

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

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

Genes
EGFR

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.2.

Table S4. 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 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

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 5p15.33.

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

Genes
TERT

Genes in Wide Peak

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

Table S10. 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 12q15.

Table S11. 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 20q13.2.

Table S12. 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 17q25.3.

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

Genes
CBX4
CBX8

Genes in Wide Peak

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

Table S14. 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 8p11.21.

Table S15. 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 6p22.3.

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

Genes
E2F3
CDKAL1

Genes in Wide Peak

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

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

Genes
CDK4
CYP27B1
METTL1
TSPAN31
MARCH9
AGAP2

Genes in Wide Peak

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

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

Genes
IGF1R
SYNM
TTC23
LRRC28
PGPEP1L
FAM169B
MIR4714

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
SNORA55
PPIEL

Genes in Wide Peak

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

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

Genes
BRD4
NOTCH3
EPHX3

Genes in Wide Peak

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

Table S21. 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 14q13.3.

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

Genes
NKX2-1
PAX9
NKX2-8
MBIP
SLC25A21
SFTA3

Genes in Wide Peak

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

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

Genes
hsa-mir-718
ABCD1
ARHGAP4
AVPR2
HCFC1
IDH3G
IRAK1
L1CAM
MECP2
PLXNB3
RENBP
SSR4
NAA10
TMEM187
SRPK3
PDZD4
MIR718
MIR3202-2
MIR3202-1

Genes in Wide Peak

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

Table S24. 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 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 13q34.

Table S26. 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 2q31.2.

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

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

Genes in Wide Peak

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

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

Genes
KRAS
CASC1
LYRM5

Genes in Wide Peak

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

Table S29. 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 5q35.3.

Table S30. 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 1q44.

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

Genes
hsa-mir-3124
ADSS
HNRNPU
ZNF124
CEP170
AKT3
ZNF238
SDCCAG8
TRIM58
AHCTF1
OR1C1
OR2M4
OR2L2
OR2L1P
OR2T1
PPPDE1
SCCPDH
KIF26B
ZNF692
ZNF695
TFB2M
SMYD3
ZNF669
ZNF672
SH3BP5L
OR2G3
OR2G2
OR2C3
EFCAB2
ZNF496
ZNF670
NLRP3
FAM36A
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
OR2B11
C1orf150
LOC148824
LOC149134
CNST
PLD5
C1orf100
OR2T6
LOC255654
C1orf101
PGBD2
OR2L13
OR14A16
HNRNPU-AS1
VN1R5
LOC339529
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
C1orf229
OR2M1P
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
OR2W5
OR13G1
LOC646627
LOC731275
MIR3124
MIR3916
ZNF670-ZNF695
MIR4677

Genes in Wide Peak

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

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

Genes
AKR1C1
AKR1C2
AKR1C3

Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 10q22.2.

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

Genes
VDAC2
KAT6B
DUSP13
ZNF503
COMTD1
SAMD8
ZNF503-AS1
DUPD1
ZNF503-AS2

Genes in Wide Peak

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

Table S34. 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 9p13.3.

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

Genes
CA9
RMRP
TLN1
TPM2
RGP1
CREB3
GBA2
C9orf100
CCDC107
MSMP

Genes in Wide Peak

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

Table S36. 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
DPP6
EN2
MNX1
HTR5A
INSIG1
PTPRN2
SHH
VIPR2
UBE3C
DNAJB6
PAXIP1
NCAPG2
WDR60
ESYT2
LMBR1
LINC00244
NOM1
C7orf13
RNF32
LOC154822
RBM33
LOC202781
CNPY1
LOC285889
MIR153-2
LOC645249
MIR595
LOC100128264
LOC100132707
LOC100506585

Genes in Wide Peak

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

Table S37. 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 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
ZNF318
YIPF3
GTPBP2
MRPS18A
TMEM63B
XPO5
MRPL14
DLK2
ABCC10
TJAP1
C6orf223
RSPH9
LRRC73
LOC100132354

Genes in Wide Peak

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

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

Genes
REL
BCL11A
OTX1
PEX13
XPO1
USP34
CCT4
B3GNT2
EHBP1
PAPOLG
FAM161A
KIAA1841
AHSA2
COMMD1
PUS10
TMEM17
LOC339803
C2orf74
FLJ16341
SNORA70B
LOC100132215
MIR4432

Genes in Wide Peak

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

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

Genes
CDK6
FAM133B
LOC728066

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 - 51 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 | chr9:21555227-22455891 | 6
19p13.3 | 3.9437e-208 | 3.9437e-208 | chr19:1171151-1272039 | 5
8p23.2 | 4.5802e-224 | 1.3928e-193 | chr8:2079140-6262191 | 1
5q11.2 | 1.0101e-170 | 2.4507e-148 | chr5:58260298-59787985 | 3
13q14.2 | 1.1622e-147 | 3.4796e-120 | chr13:48833767-49064807 | 2
10q23.31 | 1.7532e-136 | 1.4358e-117 | chr10:89615138-90034038 | 2
4q34.3 | 2.6841e-132 | 9.2019e-99 | chr4:178911874-183060693 | 1
6q26 | 7.725e-119 | 3.7678e-96 | chr6:161693099-163153207 | 1
22q13.32 | 3.8237e-83 | 3.8237e-83 | chr22:48668761-51304566 | 46
16q23.1 | 5.5542e-74 | 5.5542e-74 | chr16:78129058-79627770 | 1
11p15.5 | 1.7287e-70 | 1.7287e-70 | chr11:1-748945 | 36
2q22.1 | 5.2645e-84 | 3.5549e-65 | chr2:139655617-143637838 | 1
3p14.2 | 8.2542e-67 | 5.2294e-55 | chr3:59034763-61547330 | 1
1p36.11 | 1.6304e-129 | 3.2692e-52 | chr1:26900639-27155421 | 2
16p13.3 | 4.0369e-43 | 4.0369e-43 | chr16:5144019-7771745 | 1
4q22.1 | 9.3666e-62 | 4.9809e-42 | chr4:90844993-93240505 | 1
18q23 | 9.6629e-73 | 1.076e-38 | chr18:74678491-78077248 | 14
2q37.3 | 1.8705e-60 | 8.6251e-36 | chr2:240983601-243199373 | 40
1p36.23 | 2.5505e-129 | 6.1433e-32 | chr1:7829287-8925111 | 8
15q15.1 | 9.1691e-62 | 2.0333e-28 | chr15:41795901-42121792 | 6
17q11.2 | 4.2417e-24 | 7.5884e-24 | chr17:29326736-29722618 | 5
14q24.1 | 1.0332e-16 | 1.0332e-16 | chr14:68275375-69288431 | 2
Xp21.2 | 2.8573e-16 | 2.8605e-16 | chrX:30865118-34644819 | 4
20p12.1 | 1.2648e-15 | 1.2584e-15 | chr20:13964029-16036135 | 3
17p12 | 2.5852e-15 | 5.4856e-15 | chr17:11896630-12456081 | 3
11q25 | 1.7345e-46 | 2.1101e-13 | chr11:133400280-135006516 | 14
7p22.3 | 1.1875e-12 | 1.1875e-12 | chr7:1-1303032 | 19
6p25.3 | 1.4115e-12 | 1.4115e-12 | chr6:1608837-2252425 | 2
21q11.2 | 2.0446e-12 | 2.0361e-12 | chr21:1-15482604 | 16
19q13.32 | 8.7605e-29 | 5.3518e-09 | chr19:47332686-47561946 | 5
1p13.2 | 8.0466e-20 | 2.0138e-08 | chr1:109968411-117457733 | 101
11q22.3 | 1.0765e-35 | 4.7368e-08 | chr11:104032904-116619072 | 88
9p24.1 | 1.4941e-75 | 5.8963e-08 | chr9:7799607-12693402 | 1
18q21.2 | 5.3637e-38 | 6.1739e-08 | chr18:48514396-48705371 | 1
10q26.3 | 4.3942e-33 | 8.5422e-08 | chr10:135190263-135214343 | 1
3p25.3 | 7.8076e-18 | 9.7969e-08 | chr3:11593014-11833472 | 1
7q36.1 | 1.0698e-07 | 1.0759e-07 | chr7:151817415-152136074 | 1
8p21.2 | 3.6428e-77 | 1.2963e-07 | chr8:22785402-26607629 | 31
13q11 | 2.4302e-39 | 3.3549e-07 | chr13:1-20535070 | 10
10p15.3 | 3.2709e-05 | 3.2709e-05 | chr10:1-699088 | 3
12q24.33 | 9.3281e-17 | 0.0001276 | chr12:131692956-133851895 | 27
15q11.2 | 1.5397e-39 | 0.00013328 | chr15:1-27218028 | 136
12p13.1 | 0.00032565 | 0.00032319 | chr12:12710990-12966966 | 6
19q13.43 | 1.0584e-26 | 0.00048989 | chr19:58436230-59128983 | 32
4p16.3 | 0.0016385 | 0.0016503 | chr4:1-1243876 | 27
6q22.31 | 1.763e-21 | 0.0020256 | chr6:123955968-125232805 | 1
12q23.1 | 1.6664e-13 | 0.0053689 | chr12:99124001-100431272 | 2
5q21.3 | 4.1924e-34 | 0.013953 | chr5:83677261-118175941 | 107
9q34.13 | 0.0075302 | 0.20881 | chr9:131846162-140319469 | 187
9q34.3 | 0.0014893 | 1 | chr9:135511502-141213431 | 161
9p13.1 | 7.8934e-16 | 1 | chr9:38619152-71152237 | 50

Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
MTAP
C9orf53
DMRTA1
CDKN2B-AS1

Genes in Wide Peak

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

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

Genes
STK11
ATP5D
MIDN
CIRBP-AS1
C19orf26

Genes in Wide Peak

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

Table S43. 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 S44. 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 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 10q23.31.

Table S46. 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 4q34.3.

Table S47. 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 6q26.

Table S48. 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 22q13.32.

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

Genes
hsa-mir-3201
ACR
ARSA
CHKB
CPT1B
TYMP
MAPK11
MAPK12
SBF1
PPP6R2
ZBED4
SCO2
RABL2B
MLC1
MAPK8IP2
PLXNB2
BRD1
FAM19A5
NCAPH2
MOV10L1
MIOX
PANX2
ALG12
CRELD2
ADM2
TRABD
SELO
HDAC10
SHANK3
TUBGCP6
LOC90834
LMF2
KLHDC7B
LOC284933
RPL23AP82
C22orf34
CHKB-CPT1B
IL17REL
FAM116B
PIM3
ODF3B
SYCE3
LOC100128946
LOC100144603
MIR3201
MIR4535

Genes in Wide Peak

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

Table S50. 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 11p15.5.

Table S51. 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 2q22.1.

Table S52. 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 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 1p36.11.

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

Genes
ARID1A
PIGV

Genes in Wide Peak

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

Table S55. 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 4q22.1.

Table S56. 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 18q23.

Table S57. 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 S58. 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 1p36.23.

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

Genes
RERE
TNFRSF9
PER3
VAMP3
UTS2
PARK7
SLC45A1
ERRFI1

Genes in Wide Peak

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

Table S60. 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 S61. 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 14q24.1.

Table S62. 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 Xp21.2.

Table S63. 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 20p12.1.

Table S64. 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 S65. 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 11q25.

Table S66. 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 7p22.3.

Table S67. 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 6p25.3.

Table S68. 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 21q11.2.

Table S69. 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 19q13.32.

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

Genes
AP2S1
ARHGAP35
NPAS1
TMEM160
SNAR-E

Genes in Wide Peak

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

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

Genes
NRAS
TRIM33
RBM15
hsa-mir-320b-1
hsa-mir-4256
hsa-mir-197
ADORA3
ALX3
AMPD1
AMPD2
RHOC
ATP1A1
ATP5F1
CAPZA1
CASQ2
CD2
CD53
CD58
CHI3L2
CSF1
GNAI3
GNAT2
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
IGSF3
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
NGF
NHLH2
OVGP1
RAP1A
SLC16A1
SYCP1
TSHB
WNT2B
CSDE1
SLC16A4
LRIG2
TSPAN2
BCAS2
CEPT1
HBXIP
AP4B1
PHTF1
AHCYL1
DDX20
PTPN22
CHIA
RSBN1
ST7L
SLC22A15
LRIF1
CTTNBP2NL
FAM212B
OLFML3
AMIGO1
DCLRE1B
WDR77
EPS8L3
DENND2D
SIKE1
VANGL1
GPR61
PROK1
ATP1A1OS
FAM40A
MAB21L3
ATXN7L2
DRAM2
C1orf88
C1orf162
SYT6
RP11-165H20.1
DENND2C
UBL4B
HIPK1
AKR7A2P1
MAGI3
FAM19A3
SYPL2
CYB561D1
PPM1J
SLC6A17
MIR197
LOC440600
BCL2L15
PGCP1
CYMP
LOC643441
LOC100129269
LOC100287722
MIR320B1
MIR4256
LOC100506343

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q22.3.

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

Genes
ATM
DDX10
POU2AF1
SDHD
hsa-mir-4301
hsa-mir-34c
ACAT1
CASP1
CASP4
CASP5
CRYAB
DLAT
DRD2
FDX1
GRIA4
GUCY1A2
HSPB2
HTR3A
IL18
NCAM1
NNMT
NPAT
PPP2R1B
PTS
RDX
SLN
ZBTB16
CUL5
HTR3B
ZW10
RBM7
EXPH5
SIK2
CADM1
REXO2
TIMM8B
C11orf71
SLC35F2
RAB39A
BTG4
FAM55D
TTC12
C11orf57
ELMOD1
TEX12
ARHGAP20
USP28
CARD18
AASDHPPT
C11orf1
ALG9
TMPRSS5
BCO2
KIAA1826
DIXDC1
ZC3H12C
ALKBH8
FDXACB1
C11orf52
CARD16
C11orf93
PIH1D2
FAM55A
FAM55B
KBTBD3
CWF19L2
KDELC2
LAYN
C11orf65
ANKK1
LOC283143
C11orf53
C11orf34
C11orf87
C11orf92
C11orf88
MIR34B
MIR34C
CARD17
LOC643733
LOC643923
CLDN25
LOC100132078
LOC100288346
MIR4301
CASP12
HSPB2-C11orf52
MIR4491

Genes in Wide Peak

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

Table S73. 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 18q21.2.

Table S74. 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 10q26.3.

Table S75. 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 3p25.3.

Table S76. 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 7q36.1.

Table S77. 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 8p21.2.

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

Genes
BNIP3L
DPYSL2
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 13q11.

Table S79. 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 10p15.3.

Table S80. 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 12q24.33.

Table S81. 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 15q11.2.

Table S82. 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
NBEAP1
GABRA5
GABRB3
IPW
NDN
SNRPN
UBE3A
MKRN3
PAR5
SNURF
CYFIP1
C15orf2
MAGEL2
ATP10A
NIPA2
SNORD107
TUBGCP5
NIPA1
PAR1
LOC283683
OR4N4
HERC2P3
GOLGA6L1
GOLGA8IP
SNORD108
SNORD109A
SNORD109B
SNORD115-1
WHAMMP3
POTEB
SNORD64
PAR4
PAR-SN
LOC348120
GOLGA8E
OR4M2
OR4N3P
HERC2P2
NF1P2
LOC503519
CHEK2P2
LOC646214
CXADRP2
REREP3
LOC653061
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
GOLGA8DP
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 12p13.1.

Table S83. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
hsa-mir-613
CDKN1B
CREBL2
GPR19
APOLD1
MIR613

Genes in Wide Peak

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

Table S84. 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
ZNF256
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 4p16.3.

Table S85. 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
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 6q22.31.

Table S86. 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 12q23.1.

Table S87. 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 5q21.3.

Table S88. 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
hsa-mir-583
hsa-mir-2277
hsa-mir-9-2
hsa-mir-4280
CAMK4
CAST
CCNH
CDO1
CETN3
CHD1
AP3S1
COX7C
EFNA5
FER
GLRX
KCNN2
LNPEP
MAN2A1
MCC
MEF2C
PAM
PCSK1
PGGT1B
RASA1
SRP19
NR2F1
ST8SIA4
REEP5
ATG12
NREP
RAB9BP1
TTC37
PJA2
POLR3G
RHOBTB3
ELL2
PPIP5K2
TMED7
COMMD10
ERAP1
FLJ11235
GIN1
TRIM36
RIOK2
FEM1C
SEMA6A
ARRDC3
EPB41L4A
ERAP2
FBXL17
YTHDC2
MCTP1
NUDT12
SPATA9
TSSK1B
FAM172A
GPR98
ANKRD32
TSLP
C5orf30
SLC25A46
EPB41L4A-AS1
LYSMD3
SLCO6A1
POU5F2
STARD4
WDR36
MBLAC2
TMEM161B
ARSK
FAM81B
CCDC112
DCP2
LIX1
C5orf27
AQPEP
KIAA0825
GPR150
NBPF22P
RGMB
RFESD
FAM174A
SLCO4C1
TICAM2
MIR9-2
FLJ42709
FLJ35946
TMEM232
LOC644100
LINC00461
SNORA13
MIR583
LOC728342
LOC100129716
LOC100133050
LOC100289230
LOC100289673
TMED7-TICAM2
MIR2277
MIR4280
MIR3607
MIR3660
LOC100505678
LOC100505894

Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q34.13.

Table S89. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
ABL1
NOTCH1
RALGDS
TSC1
BRD3
NUP214
FNBP1
hsa-mir-4292
hsa-mir-126
ABCA2
ABO
ASS1
C8G
ENTPD2
CEL
CELP
COL5A1
CRAT
DBH
SARDH
TOR1A
FCN1
FCN2
FUT7
RAPGEF1
GRIN1
LCN1
PAEP
PPP2R4
PTGDS
RPL7A
RXRA
SNAPC4
SURF1
SURF2
SURF4
MED22
SURF6
TRAF2
TTF1
VAV2
LHX3
GFI1B
SSNA1
EDF1
FUBP3
CLIC3
GTF3C5
GTF3C4
MED27
PTGES
ADAMTSL2
PPP1R26
SEC16A
LAMC3
TUBB4B
UBAC1
OLFM1
AGPAT2
POMT1
SDCCAG3
USP20
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
MAN1B1
SETX
PMPCA
EXOSC2
NCS1
COBRA1
GPSM1
DKFZP434A062
GBGT1
SNORD62A
SNORD36C
SNORD36B
SNORD36A
SNORD24
NDOR1
TOR1B
METTL11A
PHPT1
ANAPC2
DPP7
OBP2B
OBP2A
MRPS2
EGFL7
PRRX2
C9orf78
FBXW5
C9orf167
EXD3
C9orf86
INPP5E
NPDC1
BARHL1
REXO4
KCNT1
GPR107
PRDM12
CARD9
DDX31
AIF1L
UCK1
NTNG2
PRRC2B
PPAPDC3
FIBCD1
KIAA1984
SNHG7
TMEM141
SAPCD2
C9orf69
UAP1L1
TMEM203
NACC2
C9orf116
LCN8
FAM69B
ASB6
SLC34A3
CAMSAP1
C9orf163
MAMDC4
LCN6
AK8
C9orf96
QSOX2
LINC00094
LCN12
C9orf142
TPRN
FAM78A
QRFP
GLT6D1
C9orf50
C9orf169
IER5L
C9orf171
LCN15
C9orf172
LRRC26
TMEM8C
LCN9
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
MIR126
C9orf106
LCN10
C9orf173
NRARP
FAM163B
RNF224
SNORA17
SNORA43
SNORD62B
RNF208
DNLZ
LOC100128593
LOC100129722
LOC100130954
LOC100131193
RNU6ATAC
LOC100272217
LOC100289341
MIR4292
MIR3621
MIR3689A
MIR3689B
LOC100506190
LOC100506599
MIR3689D1
MIR3689F
MIR4669
MIR4673
MIR4674
MIR3689C
MIR3689D2
MIR3689E
MIR4479

Genes in Wide Peak

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

Table S90. Genes in bold are cancer genes as defined by The Sanger Institute's Cancer Gene Census [7].

Genes
NOTCH1
RALGDS
TSC1
BRD3
hsa-mir-602
hsa-mir-4292
hsa-mir-126
ABCA2
ABO
C8G
CACNA1B
ENTPD2
CEL
CELP
COL5A1
DBH
SARDH
FCN1
FCN2
FUT7
GRIN1
LCN1
PAEP
PTGDS
RPL7A
RXRA
SNAPC4
SURF1
SURF2
SURF4
MED22
SURF6
TRAF2
VAV2
LHX3
GFI1B
SSNA1
EDF1
CLIC3
GTF3C5
GTF3C4
ADAMTSL2
PPP1R26
SEC16A
TUBB4B
UBAC1
OLFM1
AGPAT2
SDCCAG3
NOXA1
WDR5
C9orf9
ADAMTS13
C9orf7
SLC2A6
MAN1B1
PMPCA
COBRA1
NELF
GPSM1
DKFZP434A062
GBGT1
SNORD36C
SNORD36B
SNORD36A
SNORD24
NDOR1
PHPT1
ANAPC2
DPP7
OBP2B
OBP2A
MRPS2
EGFL7
FBXW5
C9orf167
EXD3
C9orf86
INPP5E
NPDC1
REXO4
KCNT1
CARD9
DDX31
MRPL41
EHMT1
KIAA1984
SNHG7
TMEM141
C9orf37
SAPCD2
C9orf69
UAP1L1
ARRDC1
WDR85
TMEM203
ZMYND19
NACC2
C9orf116
LCN8
FAM69B
SLC34A3
CAMSAP1
C9orf163
MAMDC4
LCN6
AK8
C9orf96
QSOX2
LINC00094
LCN12
C9orf142
TPRN
GLT6D1
PNPLA7
C9orf169
ENTPD8
LCN15
C9orf172
LRRC26
TMEM8C
LCN9
LOC401557
LCNL1
C9orf139
FAM166A
SOHLH1
MIR126
LCN10
C9orf173
NRARP
FAM163B
FLJ40292
TUBBP5
RNF224
SNORA17
SNORA43
MIR602
RNF208
DNLZ
LOC100128593
LOC100129722
LOC100130954
LOC100131193
FAM157B
RNU6ATAC
LOC100289341
MIR4292
MIR3621
MIR3689A
MIR3689B
LOC100506599
MIR3689D1
MIR3689F
MIR4669
MIR4673
MIR4674
MIR3689C
MIR3689D2
MIR3689E
MIR4479

Genes in Wide Peak

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

Table S91. 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

Arm-level results

Table 3. Get Full Table Arm-level significance table - 33 significant results found. The significance cutoff is at Q value=0.25.

Arm | # Genes | Amp Frequency | Amp Z score | Amp Q value | Del Frequency | Del Z score | Del Q value
--- | --- | --- | --- | --- | --- | --- | ---
1p | 2121 | 0.17 | -2.34 | 1 | 0.18 | 0.177 | 0.661
1q | 1955 | 0.36 | 28.5 | 0 | 0.15 | -6.36 | 1
2p | 924 | 0.21 | -5.18 | 1 | 0.09 | -21.5 | 1
2q | 1556 | 0.17 | -6.6 | 1 | 0.10 | -16.8 | 1
3p | 1062 | 0.16 | -10.6 | 1 | 0.35 | 18.8 | 0
3q | 1139 | 0.27 | 5.86 | 1.32e-08 | 0.20 | -4.75 | 1
4p | 489 | 0.08 | -23.5 | 1 | 0.33 | 10.9 | 0
4q | 1049 | 0.07 | -23.2 | 1 | 0.31 | 12.8 | 0
5p | 270 | 0.30 | 4.49 | 1.75e-05 | 0.22 | -7.24 | 1
5q | 1427 | 0.18 | -5.84 | 1 | 0.29 | 12.3 | 0
6p | 1173 | 0.19 | -5.76 | 1 | 0.21 | -2.44 | 1
6q | 839 | 0.14 | -14.3 | 1 | 0.28 | 5.49 | 4.26e-08
7p | 641 | 0.43 | 27.7 | 0 | 0.14 | -14.5 | 1
7q | 1277 | 0.40 | 29.3 | 0 | 0.12 | -13.7 | 1
8p | 580 | 0.24 | -1.6 | 1 | 0.46 | 30.4 | 0
8q | 859 | 0.40 | 24.8 | 0 | 0.19 | -7.45 | 1
9p | 422 | 0.16 | -13.4 | 1 | 0.39 | 19.6 | 0
9q | 1113 | 0.14 | -12.1 | 1 | 0.34 | 16.7 | 0
10p | 409 | 0.19 | -10.2 | 1 | 0.32 | 8.03 | 1.04e-15
10q | 1268 | 0.13 | -13.9 | 1 | 0.32 | 15.8 | 0
11p | 862 | 0.13 | -17.1 | 1 | 0.24 | -0.34 | 0.938
11q | 1515 | 0.13 | -12.2 | 1 | 0.24 | 5.28 | 1.3e-07
12p | 575 | 0.27 | 1.95 | 0.103 | 0.15 | -14.6 | 1
12q | 1447 | 0.21 | -0.872 | 1 | 0.13 | -12.5 | 1
13q | 654 | 0.20 | -6.64 | 1 | 0.38 | 18.9 | 0
14q | 1341 | 0.17 | -7.33 | 1 | 0.30 | 13.6 | 0
15q | 1355 | 0.10 | -16.6 | 1 | 0.30 | 14.2 | 0
16p | 872 | 0.22 | -2.6 | 1 | 0.27 | 3.6 | 0.000288
16q | 702 | 0.18 | -9.71 | 1 | 0.36 | 16.6 | 0
17p | 683 | 0.11 | -16.9 | 1 | 0.46 | 33.1 | 0
17q | 1592 | 0.20 | -0.912 | 1 | 0.25 | 7.22 | 5.86e-13
18p | 143 | 0.19 | -10.8 | 1 | 0.35 | 11 | 0
18q | 446 | 0.15 | -14.3 | 1 | 0.38 | 18.5 | 0
19p | 995 | 0.21 | -4.46 | 1 | 0.24 | 0.798 | 0.354
19q | 1709 | 0.22 | 3.26 | 0.0025 | 0.20 | 0.481 | 0.504
20p | 355 | 0.41 | 22.1 | 0 | 0.16 | -12.9 | 1
20q | 753 | 0.44 | 31.1 | 0 | 0.11 | -16.7 | 1
21q | 509 | 0.17 | -12.4 | 1 | 0.27 | 1.45 | 0.128
22q | 921 | 0.17 | -9.1 | 1 | 0.38 | 22.1 | 0
Xq | 1312 | 0.15 | -9.93 | 1 | 0.25 | 4.92 | 8.31e-07

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/PANCAN12-TP/3025352/2.GDAC_MergeDataFiles.Finished/PANCAN12-TP.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 4976 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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