SNP6 Copy number analysis (GISTIC2)
Breast Invasive Carcinoma (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): SNP6 Copy number analysis (GISTIC2). Broad Institute of MIT and Harvard. doi:10.7908/C12Z14C9
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 2.0.21 (Firehose task version: 127).

Summary

There were 1079 tumor samples used in this analysis: 28 significant arm-level results, 29 significant focal amplifications, and 38 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 - 29 significant amplifications found. Click the link in the last column to view a comprehensive list of candidate genes. If no genes were identified within the peak, the nearest gene appears in brackets.

Cytoband Q value Residual Q value Wide Peak Boundaries # Genes in Wide Peak
11q13.3 4.7208e-211 1.3041e-190 chr11:69412882-69487994 2
8q24.21 8.1846e-92 8.1846e-92 chr8:128676088-128770551 1
8p11.23 4.6805e-96 5.9491e-83 chr8:37492669-37604543 2
17q12 7.7157e-137 1.1412e-70 chr17:37790163-37876887 6
17q23.1 7.2744e-83 2.7286e-56 chr17:57921224-57946458 1
20q13.2 2.0617e-48 2.0617e-48 chr20:52162398-52364812 1
1q21.3 2.6922e-43 4.8882e-31 chr1:150342696-150706805 15
12q15 3.0026e-15 3.0026e-15 chr12:69265279-69983634 7
6q21 8.6364e-14 8.6364e-14 chr6:107206856-107290700 1
1p22.3 4.0796e-13 4.8121e-13 chr1:85979933-86002734 1
15q26.3 1.5643e-12 1.5643e-12 chr15:99077863-99605978 3
3q26.32 2.4412e-12 2.4412e-12 chr3:176275934-180068958 22
1q44 6.2885e-22 2.0322e-10 chr1:240820760-249250621 96
8p11.21 9.4933e-35 1.3257e-07 chr8:42155813-42256603 4
6p23 1.645e-05 1.645e-05 chr6:13030994-13889516 8
10p15.1 1.7543e-05 1.7543e-05 chr10:5242638-6398978 22
19q12 3.0608e-07 1.9064e-05 chr19:29830869-30629594 6
11q14.1 1.6388e-64 7.1987e-05 chr11:76855255-78030045 16
10q22.3 9.2314e-05 9.2314e-05 chr10:80485044-82012440 14
12p13.33 0.0001442 0.0001442 chr12:1-1862157 18
14q21.1 0.0013599 0.0013599 chr14:37950906-38203719 4
11p13 0.0013355 0.0018273 chr11:32772542-33738048 10
4q13.3 0.0030731 0.0030731 chr4:73824384-74269687 6
13q34 0.012283 0.012283 chr13:93848636-115169878 147
3p25.1 0.029977 0.029977 chr3:14685335-15111124 5
19q13.42 0.0024361 0.046199 chr19:55458008-58780088 119
19p13.12 0.069917 0.07185 chr19:15136209-15293798 5
17p11.2 0.14779 0.17949 chr17:20801837-21012802 1
5p15.33 0.19973 0.19973 chr5:1-4472523 34
Genes in Wide Peak

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

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

Genes
CCND1
ORAOV1
Genes in Wide Peak

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

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

Genes
MYC
Genes in Wide Peak

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

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

Genes
ZNF703
ERLIN2
Genes in Wide Peak

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

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

Genes
ERBB2
PNMT
TCAP
STARD3
PPP1R1B
PGAP3
Genes in Wide Peak

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

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

Genes
TUBD1
Genes in Wide Peak

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

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

Genes
ZNF217
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 1q21.3.

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

Genes
SNORA40|ENSG00000253047.1
RN7SL600P
RN7SL473P
C1orf138
LINC00568
CTSS
ECM1
ENSA
MCL1
RPRD2
ADAMTSL4
GOLPH3L
TARS2
HORMAD1
MIR4257
Genes in Wide Peak

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

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

Genes
RN7SL804P
CPM
LYZ
YEATS4
CCT2
FRS2
CPSF6
Genes in Wide Peak

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

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

Genes
MIR587
Genes in Wide Peak

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

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

Genes
DDAH1
Genes in Wide Peak

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

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

Genes
MIR4714
IGF1R
PGPEP1L
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3q26.32.

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

Genes
PIK3CA
RNA5SP149
snoU13|ENSG00000239096.1
GNB4
SNORA25|ENSG00000201957.1
RNA5SP148
SNORA18|ENSG00000200288.1
RN7SKP52
LINC00578
LINC00501
RNA5SP147
ACTL6A
NDUFB5
USP13
KCNMB2
KCNMB3
ZNF639
PEX5L
MFN1
MRPL47
ZMAT3
TBL1XR1
Genes in Wide Peak

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

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

Genes
FH
PGBD2
LYPD8
OR2T7
OR2AJ1
TRIM58
OR1C1
OR14K1
OR14A2
OR2W5
RNA5SP82
MIR3916
ZNF670
SNORA25|ENSG00000252011.1
SNORD112|ENSG00000252495.1
RN7SKP55
RN7SL148P
MIR4677
RN7SKP12
RNA5SP81
ADSS
CHML
HNRNPU
RGS7
ZNF124
KMO
EXO1
CEP170
AKT3
ZBTB18
SDCCAG8
OPN3
AHCTF1
OR2M4
OR2L2
OR2T1
DESI2
SCCPDH
KIF26B
ZNF692
ZNF695
TFB2M
SMYD3
ZNF669
ZNF672
SH3BP5L
OR2L5
OR2G3
OR2G2
OR2C3
EFCAB2
ZNF496
NLRP3
COX20
OR2M5
OR2M3
OR2T12
OR14C36
OR2T34
OR2T10
OR2T4
OR2T11
OR2B11
WDR64
GCSAML
CNST
PLD5
C1orf100
OR2T6
C1orf101
OR2L13
OR14A16
OR6F1
OR2W3
OR2T8
OR2T3
OR2T29
C1orf229
OR11L1
OR2L8
OR2AK2
OR2L3
OR2M2
OR2T33
OR2M7
OR2G6
OR2T2
OR2T5
OR14I1
OR2T27
OR2T35
MAP1LC3C
OR13G1
MIR3123
MIR3124
MIR3916
Genes in Wide Peak

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

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

Genes
IKBKB
POLB
VDAC3
DKK4
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 6p23.

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

Genes
NOL7
RN7SKP204
PHACTR1
RANBP9
SIRT5
TBC1D7
GFOD1
MCUR1
Genes in Wide Peak

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

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

Genes
DKFZP667F0711
MIR3155A
RN7SKP78
SNORA14
RN7SL445P
AKR1C7P
AKR1CL1
CALML3
AKR1C4
GDI2
IL2RA
IL15RA
PFKFB3
NET1
CALML5
ANKRD16
FAM208B
ASB13
TUBAL3
FBXO18
RBM17
UCN3
Genes in Wide Peak

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

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

Genes
C19orf12
POP4
CCNE1
URI1
PLEKHF1
VSTM2B
Genes in Wide Peak

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

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

Genes
DKFZP434E1119
CLNS1A
MYO7A
NDUFC2
PAK1
THRSP
GAB2
AAMDC
RSF1
USP35
KCTD14
ALG8
INTS4
GDPD4
AQP11
KCTD21
Genes in Wide Peak

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

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

Genes
LINC00857
PLAC9
MBL1P
NUTM2E
NUTM2B
SFTPA1
ANXA11
SFTPD
PPIF
ZMIZ1
TMEM254
EIF5AL1
ZCCHC24
SFTPA2
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: Cancer Gene Census[7].

Genes
KDM5A
LINC00942
RN7SL852P
RNU4ATAC16P
FAM138D
NINJ2
RAD52
SLC6A12
SLC6A13
ERC1
WNK1
ADIPOR2
WNT5B
CCDC77
FBXL14
B4GALNT3
IQSEC3
MIR3649
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 14q21.1.

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

Genes
SNORA42|ENSG00000200385.1
TTC6
FOXA1
MIPOL1
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 11p13.

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

Genes
CD59
C11orf91
CSTF3
HIPK3
KIAA1549L
TCP11L1
PRRG4
QSER1
DEPDC7
CCDC73
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 4q13.3.

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

Genes
SNORA3|ENSG00000221639.1
RNU6ATAC5P
RNU4ATAC9P
ALB
ANKRD17
COX18
Genes in Wide Peak

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

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

Genes
ERCC5
MIR548AR
LINC00565
LINC00452
LINC00453
LINC00454
GRK1
DCUN1D2
LINC00403
LINC00404
SNORD44
LINC00354
LINC00346
LINC00567
snoU13|ENSG00000238629.1
RN7SL783P
RN7SKP10
LINC00676
RNA5SP39
MIR1267
SNORD31
LINC00443
LINC00551
ARGLU1
LINC00460
RNA5SP38
SNORA25|ENSG00000252550.1
LINC00344
LINC00343
METTL21EP
RNY5P8
LINC00283
CCDC168
snoU13|ENSG00000238869.1
LINC00555
MIR4705
RNY1P2
MIR2681
FGF14
LINC00411
GGACT
LINC00554
snoU13|ENSG00000238305.1
SNORA25|ENSG00000201245.1
MIR4306
RNY3P6
LINC00449
MIR623
RN7SKP9
RN7SL60P
RN7SKP8
snoU13|ENSG00000238407.1
RAP2A
RNA5SP37
snoU13|ENSG00000238522.1
SNORD112|ENSG00000252154.1
RN7SKP7
LINC00359
RN7SL164P
HS6ST3
snR65|ENSG00000251901.1
RNY4P27
RNY3P8
snoU13|ENSG00000238463.1
LINC00557
LINC00391
RN7SL585P
RNA5SP36
RNA5SP35
SNORD22
ATP4B
COL4A1
COL4A2
DCT
GPR183
EFNB2
F7
F10
GAS6
GPR18
ING1
IPO5
LAMP1
LIG4
PCCA
DNAJC3
SLC10A2
SLC15A1
SOX1
TFDP1
TPP2
ZIC2
STK24
CUL4A
IRS2
PROZ
ARHGEF7
CDC16
CLDN10
ITGBL1
TM9SF2
GPC6
MBNL2
FARP1
ABCC4
TUBGCP3
TNFSF13B
SOX21
RASA3
DZIP1
MYO16
ATP11A
MCF2L
DOCK9
TGDS
OXGR1
BIVM
TMCO3
ANKRD10
RAB20
CARKD
UGGT2
PCID2
UPF3A
KDELC1
CARS2
GRTP1
TMTC4
ABHD13
ZIC5
TEX30
ADPRHL1
TEX29
SPACA7
RNF113B
GPR180
CLYBL
METTL21C
NALCN
DAOA
CHAMP1
UBAC2
TMEM255B
C13orf35
FAM155A
MIR3170
MIR4502
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 3p25.1.

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

Genes
NR2C2
CCDC174
MRPS25
C3orf20
FGD5
Genes in Wide Peak

This is the comprehensive list of amplified genes in the wide peak for 19q13.42.

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

Genes
RN7SL526P
ZNF417
ZNF814
ZNF134
ZNF548
ZNF805
ZNF264
DUXA
U3|ENSG00000252683.1
MIMT1
SMIM17
ZNF71
ZSCAN5D
ZSCAN5C
RFPL4AL1
RN7SKP109
CCDC106
TMEM238
SYT5
snoU13|ENSG00000239137.1
IL11
PEG3
PTPRH
RPL28
AURKC
TNNI3
TNNT1
ZNF17
ZNF135
ZNF154
ZNF256
ZNF211
TRAPPC2P1
ZNF274
ZNF460
U2AF2
PPP6R1
ZIM2
HSPBP1
ZNF544
UBE2S
EPN1
ZNF580
GP6
ZNF581
PPP1R12C
ZNF586
EPS8L1
ZNF444
NLRP2
ZNF416
NAT14
VN1R1
ZNF304
ZNF471
USP29
ZNF667
ZSCAN18
ZSCAN5A
ZNF329
ZNF419
ISOC2
ZNF552
ZNF671
ZNF606
BRSK1
SUV420H2
ZNF587
FIZ1
GALP
ZNF628
ZNF551
ZNF835
RDH13
ZIM3
ZNF543
COX6B2
NLRP13
NLRP8
NLRP5
ZNF787
ZFP28
C19orf18
ZNF418
TMEM190
ZNF524
ZNF784
NLRP4
ZNF542
ZNF582
ZNF583
ZNF550
ZNF579
NLRP7
ZSCAN4
NLRP11
TMEM86B
ZNF549
SSC5D
ZNF547
ZIK1
ZNF776
ZSCAN1
TMEM150B
FAM71E2
NLRP9
RFPL4A
ZSCAN5B
ZNF530
DNAAF3
ZNF773
ZNF470
ZNF749
ZNF772
SBK2
SHISA7
SGK110
ZNF587B
ZNF865
Genes in Wide Peak

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

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

Genes
NOTCH3
ILVBL
CASP14
SYDE1
OR1I1
Genes in Wide Peak

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

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

Genes
USP22
Genes in Wide Peak

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

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

Genes
NDUFS6
SDHAP3
MIR4635
ZDHHC11B
CCDC127
LRRC14B
PLEKHG4B
SDHA
SLC6A3
SLC9A3
TERT
TRIP13
PDCD6
SLC12A7
TPPP
EXOC3
IRX4
CEP72
AHRR
MRPL36
BRD9
IRX1
ZDHHC11
LPCAT1
CLPTM1L
NKD2
C5orf55
C5orf38
IRX2
SLC6A19
SLC6A18
MIR4277
MIR4457
MIR4456

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 - 38 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
11q23.3 2.6232e-59 2.6232e-59 chr11:108811192-117301939 84
13q14.2 5.6844e-51 5.6844e-51 chr13:48875329-49064807 2
8p23.2 3.5566e-48 4.0186e-47 chr8:2112968-4985851 3
1p36.13 9.7599e-47 6.8418e-39 chr1:12569022-21133098 134
19p13.3 1.4308e-35 1.4308e-35 chr19:1530034-1867911 11
3p21.31 1.5499e-31 1.5191e-31 chr3:48538628-50719344 84
10q23.31 1.7276e-36 3.8122e-30 chr10:89615138-89755074 3
11p15.5 2.1072e-19 2.1072e-19 chr11:1-549958 20
9p21.3 8.382e-27 2.1427e-17 chr9:21931610-22448737 3
17p12 3.8288e-17 3.8288e-17 chr17:11919496-12456081 2
6q27 6.1079e-23 5.3609e-17 chr6:167553035-168862573 10
15q13.1 3.3709e-15 3.4212e-15 chr15:28096454-31198928 34
4q35.1 5.7156e-15 5.7156e-15 chr4:178373557-191154276 68
2q37.3 7.1467e-12 7.1467e-12 chr2:237032275-243199373 69
7q36.1 1.7051e-10 1.6547e-10 chr7:151817415-152136074 1
17q21.31 2.809e-10 2.7653e-10 chr17:40426490-44841630 123
14q24.1 4.9949e-10 4.958e-10 chr14:65408510-89591393 177
21q11.2 5.8973e-09 5.8973e-09 chr21:1-15447211 12
16q24.3 2.4212e-08 2.4212e-08 chr16:88525832-90354753 49
6q15 1.9801e-13 3.9555e-08 chr6:81053411-99720410 81
5q11.2 2.0601e-12 1.8435e-07 chr5:53838110-60632719 44
6p25.3 2.9326e-07 2.8378e-07 chr6:1-4499427 34
18q23 6.3082e-06 6.3082e-06 chr18:67485651-78077248 43
10q26.3 2.687e-13 4.1083e-05 chr10:131759706-135534747 33
1p22.1 6.4798e-11 0.00016953 chr1:84463129-114935947 243
12p13.1 0.00055694 0.00057437 chr12:12506852-13351669 17
20p13 0.00082144 0.00083511 chr20:1-815752 18
12q24.31 1.1569e-07 0.0054577 chr12:118808682-133851895 164
4p16.3 0.015673 0.015416 chr4:1-1284820 27
19q13.32 0.016896 0.017254 chr19:46732647-47835469 30
5q21.3 4.5869e-06 0.020884 chr5:105881819-107071504 3
9p23 4.465e-07 0.020884 chr9:7887952-12687261 3
12q23.1 1.0588e-06 0.025348 chr12:99119269-100424312 3
8p11.21 0.0020359 0.038859 chr8:42883855-47750537 6
22q13.32 0.045062 0.04446 chr22:46241129-51304566 61
7p22.3 0.048612 0.048592 chr7:1-5170412 49
9q21.11 0.0017448 0.072353 chr9:38619152-71152237 57
9q34.2 0.098416 0.17284 chr9:131788669-141213431 208
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 11q23.3.

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

Genes
PCSK7
SDHD
PAFAH1B2
POU2AF1
SDHD
SCARNA11|ENSG00000252992.1
RNY4P6
ZNF259
snoU13|ENSG00000238625.1
LINC00900
snoU13|ENSG00000239153.1
ACA59|ENSG00000252870.1
snoU13|ENSG00000238724.1
ATF4P4
snosnR66
C11orf34
RNA5SP351
HSPB2
ALG9
ALG9
RN7SKP273
SIK2
RNA5SP350
SNORD39|ENSG00000264997.1
RNA5SP349
APOA1
APOA4
APOC3
CRYAB
DLAT
DRD2
FDX1
HTR3A
IL18
NCAM1
NNMT
PPP2R1B
PTS
RDX
TAGLN
ZBTB16
HTR3B
ZW10
RBM7
CEP164
SIK3
BACE1
CADM1
REXO2
TIMM8B
SIDT2
C11orf71
BTG4
NXPE4
TTC12
C11orf57
TEX12
ARHGAP20
USP28
C11orf1
TMPRSS5
BCO2
BUD13
DIXDC1
ZC3H12C
FDXACB1
C11orf52
APOA5
C11orf93
PIH1D2
NXPE1
NXPE2
LAYN
ANKK1
RNF214
C11orf53
C11orf87
C11orf92
C11orf88
MIR34B
MIR34C
CLDN25
MIR4301
MIR4491
Genes in Wide Peak

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

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

Genes
RB1
LPAR6
Genes in Wide Peak

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

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

Genes
RN7SL872P
RNA5SP251
CSMD1
Genes in Wide Peak

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

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

Genes
PAX7
SDHB
UBXN10
PLA2G2C
PLA2G2D
PLA2G5
RN7SL304P
PLA2G2E
snoU13|ENSG00000239027.1
RN7SL277P
RN7SL85P
AKR7A2
AKR7A3
MIR1290
MIR4695
snoU13|ENSG00000239020.1
PADI6
MIR3972
U1|ENSG00000228549.2
MST1L
ESPNP
CROCCP2
U1|ENSG00000233421.3
CROCCP3
C1orf134
ANO7P1
C1orf64
snoU13|ENSG00000238818.1
DDI2
AGMAT
SCARNA21|ENSG00000251866.1
C1orf195
SCARNA11|ENSG00000253085.1
RNA5SP41
PRAMEF14
PRAMEF18
C1orf158
snoU13|ENSG00000238771.1
RNU6ATAC18P
CAPZB
CASP9
CDA
CLCNKA
CLCNKB
DDOST
EPHA2
HTR6
MFAP2
NBL1
PLA2G2A
RSC1A1
ZBTB17
PRDM2
ALDH4A1
DHRS3
CROCC
PDPN
PADI2
CTRC
SPEN
EMC1
PLEKHM2
OTUD3
KAZN
DNAJC16
UBR4
ATP13A2
PADI4
SZRD1
HSPB7
PADI1
HP1BP3
CELA2B
MRTO4
PADI3
FBXO42
RNF186
FBLIM1
PQLC2
TMEM51
ARHGEF10L
CAMK2N1
NBPF1
NECAP2
RCC2
KIF17
CELA2A
PLA2G2F
PINK1
PRAMEF1
PRAMEF2
EFHD2
RSG1
MUL1
TAS1R2
ACTL8
IGSF21
FHAD1
LRRC38
AADACL3
IFFO2
KLHDC7A
VWA5B1
ARHGEF19
FAM43B
AKR7L
TMCO4
SLC25A34
AADACL4
PRAMEF5
HNRNPCL1
PRAMEF9
PRAMEF10
FAM131C
SPATA21
TMEM82
PRAMEF12
PRAMEF21
PRAMEF8
PRAMEF17
PRAMEF4
PRAMEF13
SH2D5
PRAMEF3
PRAMEF11
PRAMEF6
MINOS1
PRAMEF7
PRAMEF19
PRAMEF20
PRAMEF22
PRAMEF15
PRAMEF16
MIR3675
Genes in Wide Peak

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

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

Genes
TCF3
MIR1909
ONECUT3
UQCR11
RN7SL477P
UQCR11
MBD3
REXO1
KLF16
ATP8B3
MEX3D
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 3p21.31.

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

Genes
RNA5SP131
SEMA3B
SLC38A3
GNAT1
MIR566
RN7SL217P
MIR5193
RNA5SP130
C3orf62
RN7SL182P
NDUFAF3
MIR4793
TMEM89
MIR711
AMT
APEH
RHOA
SLC25A20
CISH
COL7A1
DAG1
CELSR3
GNAI2
GPX1
HYAL1
IMPDH2
LAMB2
MST1
MST1R
PFKFB4
PRKAR2A
QARS
SEMA3F
TCTA
UBA7
USP4
UQCRC1
IFRD2
MAPKAPK3
HYAL3
HYAL2
BSN
CACNA2D2
IP6K1
RBM6
RBM5
TRAIP
ARIH2
NPRL2
USP19
CYB561D2
TMEM115
WDR6
RASSF1
TUSC2
NAT6
GMPPB
C3orf18
ZMYND10
HEMK1
IP6K2
NCKIPSD
P4HTM
QRICH1
DALRD3
RNF123
CCDC71
SLC26A6
CAMKV
NICN1
MON1A
UCN2
LSMEM2
KLHDC8B
CCDC36
AMIGO3
CDHR4
FAM212A
MIR191
MIR425
ARIH2OS
C3orf84
MIR4271
MIR4787
Genes in Wide Peak

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

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

Genes
PTEN
SNORD74|ENSG00000200891.1
KLLN
Genes in Wide Peak

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

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

Genes
HRAS
RN7SL838P
ODF3
PSMD13
RNH1
IFITM1
IFITM3
IFITM2
PKP3
SIRT3
BET1L
SIGIRR
RIC8A
ATHL1
PTDSS2
SCGB1C1
NLRP6
ANO9
B4GALNT4
IFITM5
Genes in Wide Peak

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

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

Genes
CDKN2A
CDKN2B
C9orf53
Genes in Wide Peak

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

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

Genes
MAP2K4
MIR744
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q27.

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

Genes
MLLT4
TCP10
TTLL2
GPR31
KIF25
C6orf123
UNC93A
FRMD1
DACT2
TCP10L2
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 15q13.1.

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

Genes
RN7SL82P
U8|ENSG00000252602.1
RN7SL628P
GOLGA8H
U8|ENSG00000207430.1
ULK4P2
RN7SL796P
GOLGA8Q
RN7SL196P
GOLGA8R
U8|ENSG00000238519.1
RN7SL469P
GOLGA8T
U8|ENSG00000207432.1
ULK4P3
RN7SL673P
GOLGA8J
snoZ278
GOLGA6L7P
WHAMMP2
RN7SL719P
GOLGA8M
RN7SL829P
RN7SL238P
GOLGA8F
APBA2
TJP1
HERC2
FAM189A1
NDNL2
CHRFAM7A
ARHGAP11B
GOLGA8G
HERC2P9
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 4q35.1.

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

Genes
DUX4
RNA5SP175
RNA5SP174
HSP90AA4P
CYP4V2
SNORA31|ENSG00000253013.1
TLR3
snoU13|ENSG00000239034.1
PDLIM3
UFSP2
SNORD79
RN7SL28P
snoU13|ENSG00000239116.1
snoU13|ENSG00000238596.1
snoU13|ENSG00000238319.1
U3|ENSG00000252048.1
FAM92A1P2
RN7SKP67
RN7SKP13
LINC00290
SNORD65|ENSG00000212191.1
RNA5SP173
snoU13|ENSG00000252388.1
RNA5SP172
SLC25A4
CASP3
DCTD
F11
ACSL1
FAT1
FRG1
ING2
IRF2
KLKB1
MTNR1A
SORBS2
FAM149A
CLDN22
CDKN2AIP
TENM3
LRP2BP
STOX2
KIAA1430
TRAPPC11
MLF1IP
WWC2
SNX25
ZFP42
ENPP6
RWDD4
CCDC111
TRIML2
CCDC110
TRIML1
ANKRD37
HELT
C4orf47
DUX4L4
FRG2
DUX4L7
DUX4L6
DUX4L5
DUX4L3
DUX4L2
CLDN24
MIR1305
MIR3945
MIR4455
Genes in Wide Peak

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

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

Genes
CXXC11
RNA5SP122
MIR3133
RNPEPL1
MIR149
MIR2467
MIR4441
MIR4440
FAM132B
SNORD39|ENSG00000263723.1
RBM44
COPS8
AGXT
KIF1A
BOK
COL6A3
DTYMK
GBX2
GPC1
GPR35
HDLBP
NDUFA10
SEPT2
PDCD1
PPP1R7
PER2
LRRFIP1
HDAC4
FARP2
RAMP1
STK25
CAPN10
PASK
ATG4B
SNED1
TRAF3IP1
ANO7
PRLH
THAP4
ANKMY1
SCLY
ASB1
HES6
ACKR3
GAL3ST2
RAB17
MLPH
IQCA1
C2orf54
ILKAP
ING5
TWIST2
NEU4
MTERFD2
UBE2F
OTOS
MYEOV2
OR6B3
DUSP28
ESPNL
AQP12A
KLHL30
OR6B2
ASB18
PRR21
AQP12B
D2HGDH
MIR4269
MIR4786
Genes in Wide Peak

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

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

Genes
KMT2C
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 17q21.31.

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

Genes
BRCA1
ETV4
FAM215B
RN7SL199P
RN7SL656P
RN7SL739P
LRRC37A4P
RN7SL730P
RNA5SP443
MAP3K14
FAM187A
CCDC103
RN7SL405P
RN7SL819P
FZD2
RN7SL258P
GPATCH8
U3|ENSG00000221496.1
RN7SL507P
U3|ENSG00000221044.1
C17orf105
LINC00910
LINC00854
SNORA40|ENSG00000212149.1
RNY4P2
G6PC
AOC4P
CNTD1
CCR10
HSD17B1
MIR5010
MIR548AT
AOC2
ARL4D
ATP6V0A1
FMNL1
CRHR1
DHX8
DUSP3
EZH1
GFAP
GRN
IFI35
ITGA2B
NBR1
MAPT
ADAM11
MEOX1
MPP2
MPP3
NAGLU
NMT1
NSF
PPY
PYY
RPL27
SLC4A1
STAT3
STAT5A
MLX
TUBG1
UBTF
RND2
CNTNAP1
AOC3
BECN1
EFTUD2
PLEKHM1
LRRC37A
HDAC5
GJC1
PSME3
NBR2
RAMP2
VAT1
HEXIM1
C1QL1
RUNDC3A
FAM215A
TUBG2
COA3
PSMC3IP
SOST
ARL17A
SLC25A39
HIGD1B
ATXN7L3
WNK4
C17orf53
TMUB2
ACBD4
DCAKD
PLEKHH3
DBF4B
COASY
AARSD1
VPS25
TMEM101
G6PC3
ASB16
PLCD3
TMEM106A
SPATA32
HEXIM2
LSM12
CCDC43
CD300LG
KIF18B
RUNDC1
NAGS
FAM134C
SPPL2C
ARHGAP27
STH
KANSL1
FAM171A2
C17orf104
PTRF
LINC00671
LRRC37A2
MIR2117
ARL17B
PTGES3L
Genes in Wide Peak

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

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

Genes
TSHR
GPHN
KCNK10
GPR65
LINC00911
RNU3P3
RNU6ATAC28P
snoU13|ENSG00000238978.1
SNORA79|ENSG00000221303.1
NRXN3
RNA5SP388
RN7SL587P
SNORA46|ENSG00000212371.1
FKSG61
SAMD15
RN7SL137P
TMED8
SNORA32|ENSG00000201384.1
RN7SL356P
RN7SKP17
RN7SL747P
TGFB3
C14orf1
RNA5SP387
RNU4ATAC14P
SNORA7|ENSG00000222604.1
ISCA2
MIR4709
RN7SL530P
LIN52
ENTPD5
snoU13|ENSG00000238330.1
ACOT4
C14orf169
RN7SL586P
snoU13|ENSG00000238972.1
RN7SL683P
SNORD56B
RN7SL77P
ADAM20P1
SYNJ2BP
ADAM21P1
SNORA11|ENSG00000221060.1
SLC10A1
CCDC177|ENSG00000267909.1
CCDC177|ENSG00000255994.1
ERH
RN7SL224P
RN7SL108P
RN7SL706P
RN7SL213P
U3|ENSG00000252792.1
RN7SL369P
ATP6V1D
MIR4706
FNTB
ACTN1
ACYP1
ARG2
ZFP36L1
DIO2
DLST
EIF2S1
ESRRB
FOS
FUT8
GALC
GSTZ1
GTF2A1
LTBP2
MAX
MAP3K9
ALDH6A1
PGF
PIGH
PSEN1
ABCD4
RAD51B
SEL1L
SRSF5
SLC8A3
DPF3
NUMB
ADAM21
ADAM20
DCAF5
ALKBH1
EIF2B2
PNMA1
SPTLC2
RGS6
KIAA0247
AREL1
MED6
VTI1B
BATF
NPC2
AHSA1
ACOT2
TMED10
PTPN21
VASH1
SNW1
PCNX
TTLL5
ANGEL1
ZFYVE26
TTC9
FLRT2
SIPA1L1
DCAF4
PLEK2
MLH3
POMT2
COQ6
FCF1
RDH11
COX16
ZFYVE1
EXD2
VRTN
SLC39A9
FLVCR2
GPATCH2L
SPATA7
YLPM1
ADCK1
TMEM63C
GALNT16
PLEKHH1
ZNF410
NGB
RBM25
VIPAS39
SMOC1
IRF2BPL
MPP5
ZC2HC1C
ZC3H14
CCDC176
SLIRP
DNAL1
RPS6KL1
STON2
KIAA1737
PAPLN
ELMSAN1
NEK9
IFT43
NOXRED1
JDP2
TTC8
RDH12
PTGR2
FAM161B
C14orf166B
ISM2
CEP128
FAM71D
TMEM229B
EML5
PROX2
ZDHHC22
C14orf178
VSX2
RAB15
HEATR4
PLEKHD1
LINC00238
ACOT1
ACOT6
SYNDIG1L
MIR625
MIR1260A
MIR4505
MIR4708
MIR5694
Genes in Wide Peak

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

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

Genes
RNA5SP488
ANKRD20A11P
CYP4F29P
ANKRD30BP2
BAGE2
SNORA70|ENSG00000252199.1
RN7SL52P
TEKT4P2
MIR3648
TPTE
POTED
MIR3687
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 16q24.3.

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

Genes
CBFA2T3
FANCA
FAM157C
TUBB8P7
URAHP
TUBB3
SNORD68
SLC22A31
MIR4722
MIR5189
AFG3L1P
APRT
C16orf3
CDH15
CYBA
DPEP1
GALNS
GAS8
MC1R
MVD
CHMP1A
RPL13
SPG7
CDK10
VPS9D1
PIEZO1
TUBB3
PRDM7
TCF25
CPNE7
IL17C
ANKRD11
TRAPPC2L
DEF8
DBNDD1
CDT1
SPIRE2
CENPBD1
ZNF276
RNF166
SPATA2L
SPATA33
ZC3H18
ZNF778
ACSF3
LINC00304
SNAI3
CTU2
PABPN1L
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 6q15.

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

Genes
RN7SL509P
RN7SL797P
SNORA18|ENSG00000252249.1
U3|ENSG00000221455.1
U3|ENSG00000200492.1
RN7SL415P
RN7SKP110
CASP8AP2
snoU13|ENSG00000238747.1
RN7SL11P
RN7SL336P
SNORA73|ENSG00000222145.1
RN7SL183P
snoU13|ENSG00000238628.1
C6ORF165
RN7SKP209
RN7SL643P
SNHG5
CYB5R4
RWDD2A
SNORA70|ENSG00000206886.1
RNA5SP210
CGA
CNR1
EPHA7
GABRR1
GABRR2
HTR1E
ME1
NT5E
PGM3
POU3F2
MAP3K7
TPBG
RNGTT
TBX18
FHL5
SNAP91
SYNCRIP
SLC35A1
FUT9
PNRC1
KIAA1009
ANKRD6
DOPEY1
ZNF292
MDN1
UFL1
ORC3
IBTK
FBXL4
NDUFAF4
UBE2J1
AKIRIN2
FAM46A
RARS2
SMIM8
LYRM2
SNX14
RRAGD
BACH2
C6orf164
MANEA
GPR63
SPACA1
GJA10
UBE3D
MRAP2
KLHL32
RIPPLY2
PM20D2
SRSF12
C6orf165
PRSS35
C6orf163
MMS22L
GJB7
MIR2113
MIR4464
MIR4643
MIR548AI
Genes in Wide Peak

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

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

Genes
IL6ST
FKSG52
MIR582
GAPT
snoU13|ENSG00000238899.1
snoU13|ENSG00000238717.1
RNU6ATAC2P
RNA5SP185
RNA5SP184
snoU13|ENSG00000238326.1
RNA5SP183
MIR5687
MIR449C
MIR449B
MIR449A
GPX8
GZMK
ERCC8
GZMA
MAP3K1
PDE4D
PPAP2A
CCNO
PLK2
ESM1
SKIV2L2
PART1
DHX29
DDX4
DEPDC1B
GPBP1
ANKRD55
ELOVL7
NDUFAF2
RAB3C
SETD9
IL31RA
SLC38A9
MIER3
CDC20B
MCIDAS
ACTBL2
SMIM15
MIR548AE2
Genes in Wide Peak

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

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

Genes
IRF4
RNA5SP202
snoU13|ENSG00000252668.1
C6ORF50
RNA5SP201
C6orf195
RN7SL352P
snoU13|ENSG00000238438.1
BPHL
SERPINB1
FOXF2
FOXC1
GMDS
NQO2
SERPINB6
SERPINB9
TUBB2A
RIPK1
PRPF4B
ECI2
FAM50B
EXOC2
WRNIP1
DUSP22
SLC22A23
FOXQ1
HUS1B
PXDC1
FAM217A
MYLK4
TUBB2B
PSMG4
C6orf201
MIR4645
Genes in Wide Peak

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

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

Genes
RBFA
RBFADN
SALL3
RNA5SP461
SNORA25|ENSG00000199392.1
GALR1
LINC00683
ZNF516
SMIM21
ZADH2
RN7SL551P
RN7SL401P
MIR548AV
RNA5SP460
RN7SL795P
CYB5A
MBP
NFATC1
ZNF236
CTDP1
SOCS6
TSHZ1
CD226
TXNL4A
ADNP2
RTTN
KCNG2
TIMM21
ZNF407
CNDP2
PQLC1
NETO1
PARD6G
CNDP1
FAM69C
CBLN2
FBXO15
GTSCR1
LINC00908
ATP9B
LINC00909
HSBP1L1
C18orf63
Genes in Wide Peak

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

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

Genes
MIR3944
TUBGCP2
C10orf91
BNIP3
PPP2R2D
LINC00959
ADAM8
CYP2E1
ECHS1
INPP5A
UTF1
GLRX3
DPYSL4
VENTX
CALY
TTC40
LRRC27
GPR123
KNDC1
MTG1
SYCE1
PRAP1
ZNF511
PWWP2B
PAOX
TCERG1L
FUOM
JAKMIP3
STK32C
FRG2B
SPRN
MIR202
MIR378C
Genes in Wide Peak

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

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

Genes
BCL10
RBM15
BCL2L15
LRIG2
snoU13|ENSG00000238975.1
WNT2B
snoU13|ENSG00000238761.1
snoU13|ENSG00000239111.1
ATP5F1
PGCP1
DENND2D
RNA5SP54
CYMP
SNORA25|ENSG00000200536.1
ALX3
RNU6V
GNAI3
KIAA1324
SCARNA2
TMEM167B
TAF13
SPATA42
NBPF5P
SLC25A24P1
RN7SKP285
snoU13|ENSG00000238296.1
SCARNA16|ENSG00000252765.1
DPH5
MIR553
LPPR5
RN7SKP270
RN7SL831P
ALG14
snoU13|ENSG00000238389.1
RN7SL440P
ARHGAP29
GCLM
DNTTIP2
RNA5SP53
DR1
RN7SKP123
RN7SL692P
SNORA51|ENSG00000207022.1
SNORA66|ENSG00000207523.1
SNORA66|ENSG00000251795.1
SNORD21
RN7SL824P
RPAP2
ACTBP12
RN7SL235P
RN7SL653P
BARHL2
U3|ENSG00000199666.1
RN7SKP272
snoU13|ENSG00000239176.1
GBP1P1
GBP6
RN7SL583P
RNA5SP52
RNA5SP51
SNORD81|ENSG00000199934.1
C1orf52
CTBS
SPATA1
RPF1
UOX
SNORA2|ENSG00000199959.1
ABCA4
ADORA3
AGL
AMPD2
AMY1A
AMY1B
AMY1C
AMY2A
AMY2B
RHOC
BRDT
CAPZA1
CD53
CHI3L2
CLCA1
CNN3
COL11A1
CSF1
DBT
DPYD
S1PR1
CELSR2
EXTL2
F3
GBP1
GBP2
GBP3
GFI1
GNAT2
GNG5
GSTM1
GSTM2
GSTM3
GSTM4
GSTM5
GTF2B
CYR61
KCNA2
KCNA3
KCNA10
KCNC4
KCND3
MOV10
OVGP1
PRKACB
PKN2
PSMA5
ABCD3
RAP1A
RPL5
SORT1
SARS
SLC16A1
STXBP3
TGFBR3
VCAM1
EVI5
CDC7
BCAR3
LMO4
CDC14A
RTCA
SLC16A4
CLCA3P
CLCA2
HS2ST1
LPPR4
CEPT1
VAV3
LAMTOR5
AP4B1
PHTF1
AHCYL1
GLMN
DDX20
CLCA4
MTF2
NTNG1
WDR47
CLCC1
KIAA1107
SLC35A3
LRRC8B
LPAR3
DDAH1
RWDD3
PTPN22
CHIA
GPSM2
SLC25A24
TMED5
SH3GLB1
SNX7
GPR88
TRMT13
RSBN1
ZNHIT6
PALMD
FNBP1L
ST7L
PRPF38B
LRRC8D
PRMT6
MCOLN3
RNPC3
LRIF1
CTTNBP2NL
FAM212B
CCBL2
OLFML3
AMIGO1
ODF2L
PTBP2
DNASE2B
HIAT1
DCLRE1B
WDR77
EPS8L3
GPR61
SYDE2
ZNF644
LRRC8C
PROK1
PSRC1
STRIP1
HENMT1
GBP4
GBP5
SSX2IP
OLFM3
WDR63
SLC44A3
ATXN7L2
C1orf194
LRRC39
DRAM2
PIFO
C1orf162
SYT6
SAMD13
TMEM56
NBPF4
SLC30A7
CHIAP2
FNDC7
SASS6
HFM1
UBL4B
HIPK1
EPHX4
AKNAD1
MCOLN2
COL24A1
MAGI3
FAM19A3
FAM102B
SYPL2
CYB561D1
ZNF326
BTBD8
PPM1J
CCDC18
MYBPHL
GBP7
C1orf146
FAM69A
SLC6A17
FRRS1
MIR197
C1orf180
RBMXL1
NBPF6
MIR760
MIR378G
MIR137HG
MIR4423
Genes in Wide Peak

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

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

Genes
HTR7P1
SNORD88
GPRC5A
MIR613
DUSP16
LOH12CR2
CDKN1B
CREBL2
GPR19
HEBP1
DDX47
GPRC5D
KIAA1467
APOLD1
GSG1
LOH12CR1
MIR614
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 20p13.

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

Genes
TCF15
CSNK2A1
DEFB128
DEFB127
DEFB126
DEFB125
SOX12
RBCK1
TRIB3
NRSN2
ZCCHC3
SCRT2
SLC52A3
TBC1D20
C20orf96
SRXN1
DEFB129
DEFB132
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 12q24.31.

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

Genes
BCL7A
ANHX
ZNF891
ZNF140
RNU4ATAC12P
RNA5SP379
LRCOL1
MUC8
SNORA49
RNA5SP378
RNA5SP377
RNA5SP376
RAN
snoU13|ENSG00000238822.1
RN7SL534P
snoU13|ENSG00000238895.1
MIR3612
TMEM132C
LINC00508
LINC00507
LINC00944
LINC00943
LINC00939
TMEM132B
BRI3BP
RPL22P19
DNAH10OS
EIF2B1
SNORA9|ENSG00000206897.1
SNRNP35
RNA5SP375
RN7SL133P
MIR4304
HCAR1
SNORA9|ENSG00000252192.1
ZCCHC8
MLXIP
ORAI1
SNORA70|ENSG00000201945.1
GATC
RPS27P25
MIR4498
snoU13|ENSG00000272464.1
MIR1178
RN7SKP197
RN7SL508P
SNORA38|ENSG00000201042.1
RNA5SP374
ACADS
SCARB1
COX6A1
STX2
GOLGA3
GTF2H3
HPD
MMP17
MSI1
P2RX4
P2RX7
PLA2G1B
POLE
PRKAB1
PSMD9
PXMP2
PXN
RPLP0
CLIP1
SFSWAP
HNF1A
UBC
ZNF10
ZNF26
ZNF84
CDK2AP1
ULK1
DENR
OASL
DYNLL1
SRSF9
HCAR3
HIP1R
PIWIL1
CABP1
NCOR2
KNTC1
MLEC
RNF10
MPHOSPH9
CAMKK2
ZNF268
TMED2
GCN1L1
RAB35
CIT
FZD10
P2RX2
SETD1B
ANKLE2
SIRT4
ABCB9
RIMBP2
ATP6V0A2
HSPB8
GALNT9
ARL6IP4
POP5
ANAPC5
TRIAP1
RHOF
SBNO1
CHFR
DIABLO
PITPNM2
EP400
DHX37
FBRSL1
DDX55
SUDS3
C12orf43
VPS33A
RSRC2
AACS
NOC4L
B3GNT4
OGFOD2
VPS37B
TCTN2
RNF34
CCDC92
PUS1
COQ5
SRRM4
CCDC62
KDM2B
UNC119B
C12orf65
CCDC64
TMEM132D
SLC15A4
SPPL3
FAM101A
ZNF664
TMEM120B
WDR66
GLT1D1
CCDC60
PGAM5
RILPL2
DNAH10
LRRC43
GPR133
MORN3
DDX51
HCAR2
EP400NL
RILPL1
IL31
TMEM233
SETD8
ZNF605
MIR3908
MIR4419B
MIR4700
MIR5188
Genes in Wide Peak

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

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

Genes
SNORA48|ENSG00000212458.1
TMED11P
RN7SL358P
ZNF721
ABCA11P
MIR571
ZNF141
ZNF732
ZNF876P
ZNF718
ZNF595
ATP5I
CTBP1
DGKQ
GAK
IDUA
MYL5
PDE6B
PCGF3
SPON2
CPLX1
SLC26A1
FGFRL1
PIGG
MFSD7
TMEM175
RNF212
Genes in Wide Peak

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

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

Genes
RN7SL533P
snoU13|ENSG00000252071.1
MIR320E
RN7SL364P
C5AR1
CALM3
AP2S1
ARHGAP35
NPAS1
PPP5C
PTGIR
SLC1A5
SAE1
ZC3H4
PRKD2
CCDC9
BBC3
STRN4
TMEM160
PNMAL1
PNMAL2
HIF3A
FKRP
CCDC8
GNG8
DACT3
PRR24
IGFL1
MIR3191
PPP5D1
Genes in Wide Peak

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

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

Genes
RN7SL782P
SNORA31|ENSG00000252337.1
EFNA5
Genes in Wide Peak

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

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

Genes
RN7SL5P
SNORD27|ENSG00000251699.1
PTPRD
Genes in Wide Peak

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

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

Genes
RNA5SP366
ANKS1B
FAM71C
Genes in Wide Peak

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

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

Genes
RN7SKP41
U3|ENSG00000201329.1
POTEA
FNTA
SGK196
HGSNAT
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 22q13.32.

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

Genes
ARSA
RN7SL500P
DENND6B
TTLL8
ALG12
RN7SKP252
CDPF1
C22orf26
LINC00899
ACR
CHKB
CPT1B
TYMP
PPARA
MAPK11
MAPK12
SBF1
WNT7B
CELSR1
PPP6R2
ZBED4
SCO2
PKDREJ
RABL2B
GRAMD4
MLC1
MAPK8IP2
PLXNB2
BRD1
TBC1D22A
FAM19A5
NCAPH2
GTSE1
MOV10L1
TTC38
MIOX
TRMU
PANX2
CERK
CRELD2
ADM2
TRABD
HDAC10
SHANK3
TUBGCP6
LMF2
KLHDC7B
C22orf34
FLJ27365
LINC00898
IL17REL
MIRLET7A3
MIRLET7B
PIM3
ODF3B
SYCE3
MIR3201
MIR3619
MIR3667
MIR4763
MIR4535
Genes in Wide Peak

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

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

Genes
CARD11
RNF216P1
AP5Z1
snoU13|ENSG00000238781.1
RN7SKP130
snoU13|ENSG00000238857.1
MIR4648
GRIFIN
MIR4655
ELFN1
UNCX
MIR339
COX19
FAM20C
GNA12
GPER
LFNG
NUDT1
PDGFA
PRKAR1B
MAFK
MAD1L1
EIF3B
ADAP1
IQCE
SUN1
INTS1
SNX8
FTSJ2
GET4
CYP2W1
HEATR2
CHST12
RADIL
PAPOLB
RBAK
MICALL2
TTYH3
PSMG3
C7orf50
ZFAND2A
GPR146
AMZ1
TMEM184A
BRAT1
SDK1
FOXK1
MMD2
MIR4656
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q21.11.

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

Genes
CBWD3
PGM5P2
RNA5SP284
SNORA70|ENSG00000252878.1
RN7SL787P
RNA5SP283
RN7SL544P
SNORA70|ENSG00000252133.1
FAM27E1
RN7SL722P
SNORA70|ENSG00000252617.1
FAM27E2
RN7SL565P
RN7SL343P
FAM95B1
SNORA70|ENSG00000252724.1
RN7SL763P
FAM74A6
FAM74A2
RN7SL422P
FAM74A1
RN7SL462P
FAM74A5
RN7SL640P
FAM201A
PGM5
ZNF658
SPATA31A7
CNTNAP3
ANKRD20A1
CBWD5
FOXD4L3
FOXD4L4
SPATA31A6
FAM74A4
ANKRD20A3
ANKRD20A2
FAM27A
SPATA31A2
SPATA31A4
CBWD6
SPATA31A1
FOXD4L6
FOXD4L5
FAM27D1
SPATA31A3
SPATA31A5
CBWD7
FAM74A3
CNTNAP3B
ANKRD20A4
FOXD4L2
FAM27E3
FAM27C
FAM27B
MIR1299
MIR4477A
Genes in Wide Peak

This is the comprehensive list of deleted genes in the wide peak for 9q34.2.

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

Genes
ABL1
NOTCH1
RALGDS
TSC1
BRD3
NUP214
FNBP1
FAM157B
TUBBP5
MRPL41
snoU13|ENSG00000272272.1
RNF224
TMEM210
MIR3621
snoU13|ENSG00000238824.1
SNORD62
CLIC3
C9orf141
MIR4479
C9orf172
MIR4292
LCN10
LCN6
SNHG7
FAM69B
MIR126
U3|ENSG00000252440.1
MIR4673
DNLZ
DKFZP434A062
MIR4669
RXRA
RNU6ATAC
LINC00094
FAM163B
SNORD36C
SNORD36A
SNORD36B
SNORD24
ABO
snoU13|ENSG00000238657.1
CELP
GTF3C4
SNORA67|ENSG00000212395.1
RN7SL328P
SNORD62B
SNORD62A
PRRC2B
SNORA31|ENSG00000252582.1
snoU13|ENSG00000238298.1
RN7SL665P
HMCN2
ASB6
LINC00963
RN7SL159P
C9orf106
ABCA2
ASS1
C8G
CACNA1B
ENTPD2
CEL
COL5A1
CRAT
DBH
SARDH
TOR1A
FCN1
FCN2
FUT7
RAPGEF1
GRIN1
LCN1
PAEP
PPP2R4
PTGDS
RPL7A
SNAPC4
SURF1
SURF2
SURF4
MED22
SURF6
TRAF2
TTF1
VAV2
LHX3
GFI1B
SSNA1
EDF1
FUBP3
GTF3C5
MED27
PTGES
ADAMTSL2
PPP1R26
SEC16A
LAMC3
TUBB4B
UBAC1
OLFM1
AGPAT2
POMT1
SDCCAG3
NOXA1
USP20
WDR5
C9orf9
ADAMTS13
CACFD1
SLC2A6
MAN1B1
SETX
PMPCA
EXOSC2
NCS1
NELFB
NSMF
GPSM1
GBGT1
NDOR1
TOR1B
NTMT1
PHPT1
ANAPC2
DPP7
OBP2B
OBP2A
MRPS2
EGFL7
PRRX2
C9orf78
FBXW5
TOR4A
EXD3
RABL6
INPP5E
NPDC1
BARHL1
REXO4
DOLPP1
KCNT1
GPR107
PRDM12
DDX31
EHMT1
AIF1L
UCK1
NTNG2
PPAPDC3
FAM73B
FIBCD1
KIAA1984
TMEM141
C9orf37
SAPCD2
C9orf69
UAP1L1
ARRDC1
DPH7
TMEM203
ZMYND19
NACC2
C9orf116
LCN8
SLC34A3
CAMSAP1
C9orf62
C9orf163
MAMDC4
LCN6
AK8
C9orf96
QSOX2
LCN12
C9orf142
TPRN
FAM78A
QRFP
GLT6D1
C9orf50
PNPLA7
C9orf169
ENTPD8
IER5L
C9orf171
LCN15
LRRC26
TMEM8C
LCN9
LCNL1
C9orf139
FAM166A
SOHLH1
C9orf173
NRARP
MIR602
RNF208
CARD9
MIR3689A
MIR3689B
MIR3689D1
MIR3689F
MIR4674
MIR3689C
MIR3689D2
MIR3689E
MIR548AW
Arm-level results

Table 3.  Get Full Table Arm-level significance table - 28 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 1300 0.22 1.4 0.294 0.30 7.74 2.12e-14
1q 1195 0.65 33.1 0 0.34 7.39 2.94e-13
2p 624 0.13 -8.07 1 0.20 -3.05 1
2q 967 0.08 -10.1 1 0.21 -0.409 1
3p 644 0.14 -7.1 1 0.21 -2.26 1
3q 733 0.21 -1.95 1 0.13 -7.17 1
4p 289 0.09 -10.3 1 0.36 6.89 9.57e-12
4q 670 0.09 -9.52 1 0.31 5.51 4.6e-08
5p 183 0.31 2.91 0.00908 0.22 -3.38 1
5q 905 0.24 1.16 0.407 0.27 3.41 0.000626
6p 710 0.22 -1.1 1 0.23 -0.548 1
6q 556 0.17 -4.73 1 0.31 4.29 1.88e-05
7p 389 0.31 3.6 0.00107 0.16 -6.01 1
7q 783 0.27 2.74 0.0136 0.16 -5 1
8p 338 0.32 3.11 0.00527 0.56 20.9 0
8q 551 0.51 18.6 0 0.24 -0.166 0.984
9p 301 0.17 -5.74 1 0.34 5.61 2.62e-08
9q 700 0.14 -6.4 1 0.30 4.68 3.2e-06
10p 253 0.21 -3.96 1 0.23 -2.29 1
10q 738 0.13 -7 1 0.25 1.23 0.199
11p 509 0.16 -5.91 1 0.30 3.74 0.000186
11q 975 0.12 -6.19 1 0.37 11.8 0
12p 339 0.23 -1.87 1 0.19 -4.56 1
12q 904 0.19 -2.39 1 0.16 -4.73 1
13q 560 0.14 -6.24 1 0.44 14.1 0
14q 938 0.17 -3.19 1 0.28 4.69 3.2e-06
15q 810 0.11 -7.68 1 0.32 7.01 4.41e-12
16p 559 0.43 11.8 0 0.41 10.3 0
16q 455 0.22 -1.32 1 0.65 28.5 0
17p 415 0.14 -5.64 1 0.61 26.1 0
17q 972 0.25 2.02 0.0873 0.33 8.31 0
18p 104 0.22 -3.45 1 0.37 6.19 9.48e-10
18q 275 0.20 -4.04 1 0.35 5.91 4.89e-09
19p 681 0.20 -2.36 1 0.23 -0.714 1
19q 935 0.23 0.493 0.956 0.20 -1.34 1
20p 234 0.41 10.3 0 0.16 -6.3 1
20q 448 0.43 13.2 0 0.11 -8.54 1
21q 258 0.22 -3.29 1 0.20 -4.04 1
22q 564 0.16 -4.6 1 0.49 17.9 0
Xq 668 0.15 -6.44 1 0.21 -2.33 1
Methods & Data
Input
Description
  • Segmentation File: The segmentation file contains the segmented data for all the samples identified by GLAD, CBS, or some other segmentation algorithm. (See GLAD file format in the Genepattern file formats documentation.) It is a six column, tab-delimited file with an optional first line identifying the columns. Positions are in base pair units.The column headers are: (1) Sample (sample name), (2) Chromosome (chromosome number), (3) Start Position (segment start position, in bases), (4) End Position (segment end position, in bases), (5) Num markers (number of markers in segment), (6) Seg.CN (log2() -1 of copy number).

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

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

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

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

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

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

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

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

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

  • 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.

  • Gene GISTIC: When enabled (value = 1), this option causes GISTIC to analyze deletions using genes instead of array markers to locate the lesion. In this mode, the copy number assigned to a gene is the lowest copy number among the markers that represent the gene.

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/BRCA-TP/11446289/GDAC_MergeDataFiles_11447072/BRCA-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_GENCODE_v18_20140127.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

  • Gene GISTIC = 1

Table 4.  Get Full Table First 10 out of 1079 Input Tumor Samples.

Tumor Sample Names
TCGA-3C-AAAU-01A-11D-A41E-01
TCGA-3C-AALI-01A-11D-A41E-01
TCGA-3C-AALJ-01A-31D-A41E-01
TCGA-3C-AALK-01A-11D-A41E-01
TCGA-4H-AAAK-01A-12D-A41E-01
TCGA-5L-AAT0-01A-12D-A41E-01
TCGA-5L-AAT1-01A-12D-A41E-01
TCGA-5T-A9QA-01A-11D-A41E-01
TCGA-A1-A0SB-01A-11D-A141-01
TCGA-A1-A0SD-01A-11D-A111-01

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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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)
[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)
[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)