Counting down to the V91 release...
27 Mar 2020
In these trying times we are still producing the COSMIC v91 release for you!
There is an update to our high-quality manual curation on 4 new known cancer genes which are TRAPP, KMT2A, MYC and CDKN1B. There are substantial updates to the existing expert curated gene APC. We have also focussed on testicular and other male cancers as well as breast implant related lymphoma.
We are also updating our ICGC dataset to v28, which includes 2 new studies: ICGC( BPLL-FR ) : B-Cell Prolymphocytic Leukemia - FR and ICGC( GACA-JP ) : Gastric Cancer - JP; with a complete re-annotation using Ensembl Variant Effect Predictor (VEP).
In response to user feedback, we are providing a new mutation tracking file for COSMIC and the Cell Line Project to map the legacy COSM/COSN IDs to the new genomic ID (COSV), along with the gene names, accession number and a new unique mutation identifier. We will also indicate in the file if these mutations were coding or non-coding. There is also a field that indicates if the annotation is on the canonical transcript. We will make a taster file available to our users very soon!
We are also improving our VCF files to include HGVS syntaxes on the genomic (HGVSG), on the cds (HGVSC) to include the transcript accession number with the version and on the peptide (HGVSP) with Ensembl's peptide accession.
To our VCF files, we have added normalised version denoted with the suffix <normal>, where each variant is 5' shifted whilst maintaining the HGVS compliant (3’ shifted) syntaxes in the INFO section. This reflects the non-normalised version where different. We have also compressed these files with bgzip following user feedback.
All our files with the mutation syntaxes have got these additional columns of HGVSG, HGVSC and HGVSP. If you want a list of these files now, please contact us at firstname.lastname@example.org.
Our aim is to get the v91 release out in the next two weeks so keep a look-out!
If you have any suggestions for content or functionality that you would like to see in a coming release, please contact us at email@example.com.