Provides accurate frequency data as mutation negative samples areĪlso called non-systematic or targeted screen data Includes additional data points relevant to each disease and Manually input from peer reviewed publications by COSMIC expertĬonsists of comprehensive literature curation of selectedĪ given release then updated at subsequent releases These data types and use them appropriately. It is useful to understand the differences of There are two types of data in COSMIC: expert manual curation data and We recognise the additional value of these transcript level c.* annotations from manual curation and we areĬurrently working to reincorporate them, but at the moment there is no release date. Transcript level (and given TERT c.-124C>T style syntaxes) were converted to COSN mutations identified with Mutations, which had previously been annotated at the However, one unintended consequence of the upgrade in v90 was that the manually curated TERT promoter syntax), as this is a standard annotation for non-coding mutations processed from whole genome

TERT promoter mutations from whole genome screens have always been curated in COSMIC using genomic annotations Of mutations is now standardised using Ensembl VEP using the latest HGVS rules. Mutations to a more recent and defined set of transcripts (Gencode basic, Ensembl release 93). This enabled us to standardise annotations and map There was a major upgrade to the annotation system in v90. Why aren’t TERT promoter mutations showing under the TERT gene or sample specific pages? In a future release we plan to replace the SNP flag with an allele frequency. In v95 we will partially address point 3 by removing the SNP flag from the mutation downloadsĪnd the website. In August 2020 (v92) we addressed points 1 and 2 by including all mutations, including those flagged as SNPs,

The SNP panel isn't current and over time tracing the origin of SNPs in the panel has become very difficult.

It is preferable for the website and download datasets to be the same.

User defined filtering is preferable to excluding data.

While variants flagged as SNPs were excluded from the website they were still included in the mutationĭownloads but with the SNP flag (y/n) shown.This strategy continued until 2020 but began to change as a result Variants reported in whole genome screens were matched to an internal SNP panel defined from theġ000 Genomes Project and normal (non-cancer) samples sequenced at Sanger. June 2014 (v69) we introduced a 'noise reduction' strategy for whole genome screens which included SNPįiltering.

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