cancer: blca file: broad.mit.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level2-dedup.maf Sequencing tech: Illumina GAIIx Center: broad.mit.edu Datatype level: 2 NCBI Build: 37 # samples: 28 # variants: 11026 -- Variant Classification breakdown -- 534 3'UTR 61 5'Flank 253 5'UTR 1 De_novo_Start_InFrame 1 De_novo_Start_OutOfFrame 110 Frame_Shift_Del 55 Frame_Shift_Ins 319 IGR 39 In_Frame_Del 6 In_Frame_Ins 1655 Intron 5197 Missense_Mutation 458 Nonsense_Mutation 9 Nonstop_Mutation 157 RNA 2037 Silent 125 Splice_Site 9 Translation_Start_Site -- Validation Status breakdown -- 11026 Somatic cancer: brca file: genome.wustl.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level2-dedup.maf Sequencing tech: Illumina GAIIx Center: genome.wustl.edu Datatype level: 2 NCBI Build: 36 37 # samples: 514 # variants: 41727 -- Variant Classification breakdown -- 1403 Frame_Shift_Del 439 Frame_Shift_Ins 549 In_Frame_Del 124 In_Frame_Ins 24928 Missense_Mutation 1922 Nonsense_Mutation 36 Nonstop_Mutation 2320 RNA 9199 Silent 807 Splice_Site -- Validation Status breakdown -- 41708 Unknown Somatic 19 Unknown Unknown cancer: cesc file: broad.mit.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level2-dedup.maf Sequencing tech: Illumina GAIIx Center: broad.mit.edu Datatype level: 2 NCBI Build: 37 # samples: 36 # variants: 9966 -- Variant Classification breakdown -- 105 3'UTR 57 5'Flank 60 5'UTR 21 Frame_Shift_Del 18 Frame_Shift_Ins 325 IGR 9 In_Frame_Del 1 In_Frame_Ins 2088 Intron 4772 Missense_Mutation 463 Nonsense_Mutation 11 Nonstop_Mutation 46 RNA 1905 Silent 85 Splice_Site -- Validation Status breakdown -- 9966 Somatic cancer: coad file: hgsc.bcm.edu__ABI_SOLiD_DNA_System_Sequencing_level2-dedup.maf Sequencing tech: SOLID Center: hgsc.bcm.edu Datatype level: 2 NCBI Build: 36 # samples: 53 # variants: 11577 -- Variant Classification breakdown -- 97 Frame_Shift_Del 265 Frame_Shift_Ins 55 In_Frame_Del 10 In_Frame_Ins 7598 Missense_Mutation 537 Nonsense_Mutation 3001 Silent 14 Splice_Site -- Validation Status breakdown -- 1788 Unknown Somatic 47 Valid Germline 9198 Valid Somatic 544 Wildtype None cancer: coad file: hgsc.bcm.edu__ABI_SOLiD_DNA_System_Sequencing_level3-dedup.maf Sequencing tech: SOLID Center: hgsc.bcm.edu Datatype level: 3 NCBI Build: 36 # samples: 53 # variants: 9197 -- Variant Classification breakdown -- 33 Frame_Shift_Del 131 Frame_Shift_Ins 27 In_Frame_Del 6320 Missense_Mutation 468 Nonsense_Mutation 2207 Silent 11 Splice_Site -- Validation Status breakdown -- 9197 Valid Somatic cancer: coad file: hgsc.bcm.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level2-dedup.maf Sequencing tech: Illumina HiSeq Center: hgsc.bcm.edu Datatype level: 2 NCBI Build: 36 # samples: 53 # variants: 26865 -- Variant Classification breakdown -- 14 De_novo_Start_InFrame 84 De_novo_Start_OutOfFrame 664 Frame_Shift_Del 335 Frame_Shift_Ins 61 In_Frame_Del 7 In_Frame_Ins 17563 Missense_Mutation 1470 Nonsense_Mutation 12 Nonstop_Mutation 10 RNA 6604 Silent 40 Splice_Site 1 Translation_Start_Site -- Validation Status breakdown -- 4187 Unknown Somatic 44 Valid Germline 2 Valid LOH 22149 Valid Somatic 483 Wildtype None cancer: coad file: hgsc.bcm.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level3-dedup.maf Sequencing tech: Illumina HiSeq Center: hgsc.bcm.edu Datatype level: 3 NCBI Build: 36 # samples: 52 # variants: 22149 -- Variant Classification breakdown -- 6 De_novo_Start_InFrame 62 De_novo_Start_OutOfFrame 297 Frame_Shift_Del 71 Frame_Shift_Ins 18 In_Frame_Del 2 In_Frame_Ins 15235 Missense_Mutation 1303 Nonsense_Mutation 9 Nonstop_Mutation 8 RNA 5127 Silent 11 Splice_Site -- Validation Status breakdown -- 22149 Valid Somatic cancer: gbm file: broad.mit.edu__Applied_Biosystems_Sequence_data_level2-dedup.maf Sequencing tech: Center: broad.mit.edu Datatype level: 2 NCBI Build: 36.1 # samples: 149 # variants: 13510 -- Variant Classification breakdown -- 487 Frame_Shift_Del 235 Frame_Shift_Ins 151 In_Frame_Del 89 In_Frame_Ins 5724 Missense_Mutation 71 Nonsense_Mutation 6086 Silent 280 Splice_Site_Indel 387 Splice_Site_SNP -- Validation Status breakdown -- 7904 Unknown Germline 918 Unknown LOH 1969 Unknown Somatic 573 Unknown Unknown 1611 Valid Germline 96 Valid LOH 437 Valid Somatic 2 Valid Unknown cancer: gbm file: broad.mit.edu__Applied_Biosystems_Sequence_data_level3-dedup.maf Sequencing tech: Center: broad.mit.edu Datatype level: 3 NCBI Build: 36.1 # samples: 126 # variants: 436 -- Variant Classification breakdown -- 298 Missense_Mutation 26 Nonsense_Mutation 98 Silent 14 Splice_Site_SNP -- Validation Status breakdown -- 436 Valid Somatic cancer: gbm file: genome.wustl.edu__Applied_Biosystems_Sequence_data_level2-dedup.maf Sequencing tech: Center: genome.wustl.edu Datatype level: 2 NCBI Build: 36 # samples: 160 # variants: 84368 -- Variant Classification breakdown -- 4 1 3_prime_flanking_region 5 3_prime_untranslated_region 3 5_prime_flanking_region 2 5_prime_untranslated_region 44 Frame_Shift_Del 45 Frame_Shift_Ins 19 In_Frame_Del 8 In_Frame_Ins 1 intronic 6 Intronic 4 Missense 33535 Missense_Mutation 406 Nonsense_Mutation 8 Nonstop_Mutation 44556 Silent_Mutation 6 Splice_Region_Del 2 Splice_Region_Ins 563 Splice_Site 5 Splice_Site_Del 5145 Unknown -- Validation Status breakdown -- 4 LOH 2 Unknown 59715 Unknown Germline 8869 Unknown LOH 1608 Unknown Somatic 47 Unknown Unknown 11318 Unknown Variant 1152 Valid Germline 1106 Valid LOH 437 Valid Somatic 2 Valid Unknown 108 Valid Variant cancer: gbm file: genome.wustl.edu__Applied_Biosystems_Sequence_data_level3-dedup.maf Sequencing tech: Center: genome.wustl.edu Datatype level: 3 NCBI Build: 36 # samples: 110 # variants: 436 -- Variant Classification breakdown -- 21 Frame_Shift_Del 5 Frame_Shift_Ins 8 In_Frame_Del 1 In_Frame_Ins 3 Missense 261 Missense_Mutation 23 Nonsense_Mutation 98 Silent_Mutation 11 Splice_Site 1 Splice_Site_Del 4 Unknown -- Validation Status breakdown -- 436 Valid Somatic cancer: gbm file: hgsc.bcm.edu__Applied_Biosystems_Sequence_data_level2-dedup.maf Sequencing tech: Center: hgsc.bcm.edu Datatype level: 2 NCBI Build: 36 # samples: 154 # variants: 15302 -- Variant Classification breakdown -- 10 frame_shift 59 in_frame_deletion 62 in_frame_insertion 2760 Missense 4437 Missense_Mutation 11 Nonsense 140 Nonsense_Mutation 3881 Silent 4 Splice_site 29 Splice_Site_SNP 3909 Synonymous -- Validation Status breakdown -- 13091 Unknown Germline 359 Unknown LOH 1003 Unknown Somatic 120 Valid Germline 278 Valid LOH 451 Valid Somatic cancer: gbm file: hgsc.bcm.edu__Applied_Biosystems_Sequence_data_level3-dedup.maf Sequencing tech: Center: hgsc.bcm.edu Datatype level: 3 NCBI Build: 36 # samples: 112 # variants: 450 -- Variant Classification breakdown -- 4 Missense 353 Missense_Mutation 26 Nonsense_Mutation 56 Silent 11 Splice_Site_SNP -- Validation Status breakdown -- 450 Valid Somatic cancer: kirc file: broad.mit.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level2-dedup.maf Sequencing tech: Illumina GAIIx Center: broad.mit.edu Datatype level: 2 NCBI Build: 37 # samples: 184 # variants: 30564 -- Variant Classification breakdown -- 1476 3'UTR 318 5'Flank 552 5'UTR 280 Frame_Shift_Del 65 Frame_Shift_Ins 3176 IGR 62 In_Frame_Del 5 In_Frame_Ins 9563 Intron 9875 Missense_Mutation 703 Nonsense_Mutation 14 Nonstop_Mutation 524 RNA 3615 Silent 306 Splice_Site 30 Translation_Start_Site -- Validation Status breakdown -- 30564 Somatic cancer: laml file: genome.wustl.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level2-dedup.maf Sequencing tech: Illumina GAIIx Illumina HiSeq Center: genome.wustl.edu Datatype level: 2 NCBI Build: 36 # samples: 74 # variants: 2272 -- Variant Classification breakdown -- 46 Frame_Shift_Del 66 Frame_Shift_Ins 60 In_Frame_Del 49 In_Frame_Ins 1249 Missense_Mutation 88 Nonsense_Mutation 160 RNA 501 Silent 53 Splice_Site -- Validation Status breakdown -- 1536 Unknown Somatic 736 Valid Somatic cancer: laml file: genome.wustl.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level3-dedup.maf Sequencing tech: Illumina GAIIx Illumina HiSeq Center: genome.wustl.edu Datatype level: 3 NCBI Build: 36 # samples: 59 # variants: 735 -- Variant Classification breakdown -- 14 Frame_Shift_Del 31 Frame_Shift_Ins 2 In_Frame_Del 20 In_Frame_Ins 427 Missense_Mutation 39 Nonsense_Mutation 20 RNA 166 Silent 16 Splice_Site -- Validation Status breakdown -- 735 Valid Somatic cancer: luad file: broad.mit.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level2-dedup.maf Sequencing tech: Illumina GAIIx Center: broad.mit.edu Datatype level: 2 NCBI Build: 37 # samples: 241 # variants: 247537 -- Variant Classification breakdown -- 4686 3'UTR 2889 5'Flank 2427 5'UTR 1772 Frame_Shift_Del 661 Frame_Shift_Ins 39369 IGR 250 In_Frame_Del 34 In_Frame_Ins 91890 Intron 68029 Missense_Mutation 5558 Nonsense_Mutation 65 Nonstop_Mutation 2043 RNA 25520 Silent 2188 Splice_Site 156 Translation_Start_Site -- Validation Status breakdown -- 247537 Somatic cancer: lusc file: broad.mit.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level2-dedup.maf Sequencing tech: Illumina GAIIx Center: broad.mit.edu Datatype level: 2 NCBI Build: 37 # samples: 178 # variants: 118765 -- Variant Classification breakdown -- 1054 3'UTR 1289 5'Flank 496 5'UTR 1 De_novo_Start_InFrame 1 De_novo_Start_OutOfFrame 548 Frame_Shift_Del 143 Frame_Shift_Ins 18308 IGR 9 Indel 99 In_Frame_Del 20 In_Frame_Ins 26768 Intron 46763 Missense_Mutation 4057 Nonsense_Mutation 60 Nonstop_Mutation 676 RNA 17107 Silent 1338 Splice_Site 28 Translation_Start_Site -- Validation Status breakdown -- 118765 Somatic cancer: ov file: broad.mit.edu__Applied_Biosystems_Sequence_data_level2-dedup.maf Sequencing tech: Center: broad.mit.edu Datatype level: 2 NCBI Build: 36.1 # samples: 24 # variants: 658 -- Variant Classification breakdown -- 9 Frame_Shift_Del 78 Frame_Shift_Ins 5 In_Frame_Del 6 In_Frame_Ins 269 Missense_Mutation 5 Nonsense_Mutation 256 Silent 19 Splice_Site_Indel 11 Splice_Site_SNP -- Validation Status breakdown -- 452 Unknown Germline 88 Unknown LOH 46 Unknown Somatic 23 Unknown Unknown 25 Valid Germline 3 Valid LOH 21 Valid Somatic cancer: ov file: broad.mit.edu__Applied_Biosystems_Sequence_data_level3-dedup.maf Sequencing tech: Center: broad.mit.edu Datatype level: 3 NCBI Build: 36.1 # samples: 15 # variants: 20 -- Variant Classification breakdown -- 16 Missense_Mutation 2 Nonsense_Mutation 1 Silent 1 Splice_Site_SNP -- Validation Status breakdown -- 20 Valid Somatic cancer: ov file: broad.mit.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level2-dedup.maf Sequencing tech: Illumina GAIIx Center: broad.mit.edu Datatype level: 2 NCBI Build: 36 # samples: 148 # variants: 19733 -- Variant Classification breakdown -- 328 Frame_Shift_Del 83 Frame_Shift_Ins 162 In_Frame_Del 32 In_Frame_Ins 13389 Missense_Mutation 835 Nonsense_Mutation 22 Nonstop_Mutation 4454 Silent 426 Splice_Site 2 Translation_Start_Site -- Validation Status breakdown -- 32 Germline 6404 Unknown Unknown 32 Valid Germline 12615 Valid Somatic 650 Wildtype None cancer: ov file: broad.mit.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level3-dedup.maf Sequencing tech: Illumina GAIIx Center: broad.mit.edu Datatype level: 3 NCBI Build: 36 # samples: 142 # variants: 12615 -- Variant Classification breakdown -- 158 Frame_Shift_Del 32 Frame_Shift_Ins 52 In_Frame_Del 2 In_Frame_Ins 8667 Missense_Mutation 572 Nonsense_Mutation 14 Nonstop_Mutation 2848 Silent 268 Splice_Site 2 Translation_Start_Site -- Validation Status breakdown -- 12615 Valid Somatic cancer: ov file: genome.wustl.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level2-dedup.maf Sequencing tech: ABI 3730xl Illumina GAIIx Center: genome.wustl.edu Datatype level: 2 NCBI Build: 36 # samples: 230 # variants: 18980 -- Variant Classification breakdown -- 346 Frame_Shift_Del 74 Frame_Shift_Ins 146 In_Frame_Del 25 In_Frame_Ins 11936 Missense_Mutation 688 Nonsense_Mutation 15 Nonstop_Mutation 970 RNA 4384 Silent 396 Splice_Site -- Validation Status breakdown -- 1016 Unknown Germline 11588 Unknown Somatic 15 Valid Germline 1 Valid LOH 6199 Valid Somatic 161 Wildtype None cancer: ov file: genome.wustl.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level3-dedup.maf Sequencing tech: ABI 3730xl Illumina GAIIx Center: genome.wustl.edu Datatype level: 3 NCBI Build: 36 # samples: 88 # variants: 6198 -- Variant Classification breakdown -- 76 Frame_Shift_Del 15 Frame_Shift_Ins 38 In_Frame_Del 1 In_Frame_Ins 4120 Missense_Mutation 247 Nonsense_Mutation 6 Nonstop_Mutation 274 RNA 1277 Silent 144 Splice_Site -- Validation Status breakdown -- 6198 Valid Somatic cancer: ov file: hgsc.bcm.edu__ABI_SOLiD_DNA_System_Sequencing_level2-dedup.maf Sequencing tech: SOLID Center: hgsc.bcm.edu Datatype level: 2 NCBI Build: 36 # samples: 91 # variants: 4622 -- Variant Classification breakdown -- 241 Frame_Shift_Del 114 Frame_Shift_Ins 52 In_Frame_Del 27 In_Frame_Ins 2993 Missense_Mutation 195 Nonsense_Mutation 902 Silent 96 Splice_Site 2 Splice_Site_SNP -- Validation Status breakdown -- 108 Unknown Germline 1 Unknown None 1128 Unknown Somatic 183 Valid Germline 118 Valid LOH 2457 Valid Somatic 627 Wildtype None cancer: ov file: hgsc.bcm.edu__ABI_SOLiD_DNA_System_Sequencing_level3-dedup.maf Sequencing tech: SOLID Center: hgsc.bcm.edu Datatype level: 3 NCBI Build: 36 # samples: 91 # variants: 2456 -- Variant Classification breakdown -- 14 Frame_Shift_Del 1 Frame_Shift_Ins 7 In_Frame_Del 1765 Missense_Mutation 106 Nonsense_Mutation 506 Silent 57 Splice_Site -- Validation Status breakdown -- 2456 Valid Somatic cancer: ov file: hgsc.bcm.edu__Applied_Biosystems_Sequence_data_level2-dedup.maf Sequencing tech: SOLID Center: hgsc.bcm.edu Datatype level: 2 NCBI Build: 36 # samples: 22 # variants: 860 -- Variant Classification breakdown -- 19 Frame_Shift_Del 18 Frame_Shift_Ins 18 In_Frame_Del 6 In_Frame_Ins 521 Missense_Mutation 20 Nonsense_Mutation 246 Silent 8 Splice_Site 1 Splice_Site_Indel 3 Splice_Site_SNP -- Validation Status breakdown -- 274 Unknown Germline 187 Unknown Somatic 40 Valid Germline 28 Valid LOH 271 Valid Somatic 60 Wildtype None cancer: prad file: broad.mit.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level2-dedup.maf Sequencing tech: Illumina GAIIx Center: broad.mit.edu Datatype level: 2 NCBI Build: 37 # samples: 83 # variants: 12280 -- Variant Classification breakdown -- 685 3'UTR 167 5'Flank 240 5'UTR 155 Frame_Shift_Del 81 Frame_Shift_Ins 974 IGR 54 In_Frame_Del 13 In_Frame_Ins 4298 Intron 3433 Missense_Mutation 187 Nonsense_Mutation 5 Nonstop_Mutation 320 RNA 1543 Silent 111 Splice_Site 14 Translation_Start_Site -- Validation Status breakdown -- 12280 Somatic cancer: read file: hgsc.bcm.edu__ABI_SOLiD_DNA_System_Sequencing_level2-dedup.maf Sequencing tech: SOLID Center: hgsc.bcm.edu Datatype level: 2 NCBI Build: 36 # samples: 35 # variants: 9459 -- Variant Classification breakdown -- 21 Frame_Shift_Del 34 Frame_Shift_Ins 6 In_Frame_Del 5 In_Frame_Ins 6438 Missense_Mutation 972 Nonsense_Mutation 1972 Silent 11 Splice_Site -- Validation Status breakdown -- 518 Unknown Somatic 12 Valid Germline 2 Valid LOH 8768 Valid Somatic 159 Wildtype None cancer: read file: hgsc.bcm.edu__ABI_SOLiD_DNA_System_Sequencing_level3-dedup.maf Sequencing tech: SOLID Center: hgsc.bcm.edu Datatype level: 3 NCBI Build: 36 # samples: 35 # variants: 8768 -- Variant Classification breakdown -- 7 Frame_Shift_Del 10 Frame_Shift_Ins 2 In_Frame_Del 1 In_Frame_Ins 6224 Missense_Mutation 948 Nonsense_Mutation 1567 Silent 9 Splice_Site -- Validation Status breakdown -- 8768 Valid Somatic cancer: read file: hgsc.bcm.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level2-dedup.maf Sequencing tech: Illumina HiSeq Center: hgsc.bcm.edu Datatype level: 2 NCBI Build: 36 # samples: 12 # variants: 2569 -- Variant Classification breakdown -- 3 De_novo_Start_InFrame 16 De_novo_Start_OutOfFrame 102 Frame_Shift_Del 47 Frame_Shift_Ins 17 In_Frame_Del 1619 Missense_Mutation 127 Nonsense_Mutation 2 Nonstop_Mutation 629 Silent 7 Splice_Site -- Validation Status breakdown -- 810 Unknown Somatic 1 Valid Germline 1716 Valid Somatic 42 Wildtype None cancer: read file: hgsc.bcm.edu__Illumina_Genome_Analyzer_DNA_Sequencing_level3-dedup.maf Sequencing tech: Illumina HiSeq Center: hgsc.bcm.edu Datatype level: 3 NCBI Build: 36 # samples: 12 # variants: 1716 -- Variant Classification breakdown -- 1 De_novo_Start_InFrame 7 De_novo_Start_OutOfFrame 80 Frame_Shift_Del 18 Frame_Shift_Ins 10 In_Frame_Del 1176 Missense_Mutation 94 Nonsense_Mutation 329 Silent 1 Splice_Site -- Validation Status breakdown -- 1716 Valid Somatic