Mutation Summary

Created By Kyle Ellrott kellrott
Table of Curated MAF files that are part of the Pancancer Freeze Notes The 16th column in the MAFs list the tumor sample barcode in the form "TCGA-02-0021-01A-01D-0002-04", where "TCGA-02-0021-01" indicates a distinct sample. Different barcodes may be used for the same sample, if they were sequenced several times or by several centers. Be careful not to treat their variants as observed recurrence across patients. Reducing the tumor IDs to the form "TCGA-02-0021-01" is useful to enumerate the number of tumors studied, or to de-duplicate variants from the same tumor. More information on TCGA Barcodes can be found at: https://wiki.nci.nih.gov/display/TCGA/TCGA+Barcode https://tcga-data.nci.nih.gov/datareports/codeTablesReport.htm To re-annotate variants in a MAF (e.g. using Ensembl VEP), lookup column 4 for the reference sequence used, columns 5-7 for genomic loci, and columns 11-13 for reference and variant alleles. The variant alleles in columns 12 and 13 are not always reliable to determine zygosity. The one that differs from the reference allele (column 11), is the variant allele, which may either be heterozygous or homozygous. Of the 200 sequenced LAML tumors, 3 had no reported mutations, so you won't find them listed in the MAF. Almost everything in the MAFs are from targeted exome sequencing. But 50 of the 200 LAML tumors were whole-genome sequenced, and later validated with custom capture arrays. Per-bp coverage status can be found at syn1695394. This is useful to determine regions with low coverage. You'll find several cases with lesser exome coverage in older projects like GBM and OV. Four of the tumors in the BRCA MAF are actually metastases of four other primary tumors in the same MAF. Whitelisted Maf Files