As you may remember, six months ago COSMIC launched new, improved beta download files. These new files contain the same gold standard data found in COSMIC's current files, but presented in a more accessible and interoperable manner. COSMIC aims to to lead by example in encouraging data to be FAIR (Findable, Accessible, Interoperable and Reusable) compliant, and as part of this goal, COSMIC will be phasing out its current files for COSMIC v100. We want to help make this transition as smooth as possible, so keep reading to find out what changes have been made, why they've been made, and how these changes will benefit you.

The main benefits for you!

• Increased interoperability between data sets: → IDs assigned for genes, mutations, samples and more
• Increased findability of data by gene, classification or samples: → Stable IDs between versions

What does "beta" mean?

These new files have been named "Beta" to help you distinguish them from the files you are used to, but they represent the final version and the content and layout are stable.

What's new?

1. A new, clear, consistent naming convention which all files follow
   • Full project name with no abbreviations
   • Release version and assembly clearly included
2. Each project and product have been packaged with ReadMe files individually
3. Refined columns within the files
   • Repetitive columns removed
   • Empty columns removed
4. Improved IDs
   • Consistent across both web pages, download files and webpages
   • We now have 10 COSMIC identifiers: COSMIC Phenotype Id (COSO), COSMIC Gene Id (COSG), COSMIC Sample Id (COSS), COSMIC Structural Id (COST), COSMIC CNV Id (COSCNV), COSMIC Fusion Id (COSF), Legacy Mutation Id (COSM/COSN), COSMIC Paper Id (COSP), COSMIC Study Id (COSU), COSMIC Genomic Mutation Id (COSV).

Phase out timeline

We will be phasing out current file formats in May 2024 in line with release v100, meaning that, we will be retiring our current download files and only the new style files will be available to download.

Transition support

With this in mind, here’s how the COSMIC team is helping to ease this transition:

• For the v99 update, both file types are available to download
• You can watch our recent on-demand Labroots webinar for more detailed information on the exact changes made
• Register for our latest Labroots webinar and submit your burning questions to be answered by our expert panel
• You can contact the COSMIC team directly for support here (they'd love to hear from you!)

→ Get the details on COSMIC's latest release here.

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The Cancer Gene Census (CGC) catalogues genes with mutations causally implicated in cancer and explains how dysfunction of these genes drives cancer.

New genes and annotations

With COSMIC v99, new high-quality genes have been added to the CGC ─ three to Tier 1 and three to Tier 2. The genes are HGF, RAD50, RRAS2, GSK3B, MUC6 and RAP1B.

More, cancer hallmark annotations have been added to each of the 8 existing CGC Tier 1 genes (SRC, SRSF2, STAT3, STAT5B, STK11, SUFU, TBX3, TNFRSF14). Cancer hallmark annotations summarize the effect of Tier 1 genes on the phenotypic traits shared by cancers.

Tier changes

The CGC has been compiled over 19 years and is periodically reviewed. This ensures that gene assignment to the Census reflects the latest evidence indicative of the strength of a causal association between a gene and one, or more, cancer types, and consistency in the application of the COSMIC inclusion criteria for CGC Tier 1 and Tier 2 assignment. Based on this, and following a recent review, TSHR has been re-assigned from Tier 1 of the Census to Tier 2, and its previous designation as an oncogene rescinded.

What else is new in COSMIC v99?

• 32 new systematic screen papers
• 5 manually curated cancer genes ─ IKZF3, ARHGAP35, BAX, ASPM, GSK3B
• 438,063 new genomic variants, +1 million new coding mutations, 274,853 new non-coding mutations, 6,810 new samples and 1,303 new whole genomes
• Updated Cancer Mutation Census (CMC) data that aligns with the latest COSMIC

→ Want more details? Read the full COSMIC v99 release notes here.

Gentle reminder: make the switch to COSMIC's new, improved download files

v99 is the second release available through COSMIC's new, improved download files. These new files contain the same gold standard COSMIC data found in its current files, but presented in a more accessible and interoperable manner.

What’s new?

1. A new, clear, consistent naming convention which all files follow. 
2. Each project and product have been packaged with ReadMe files individually.
3. Refined columns within the files.
4. Improved IDs which are consistent across both download files and webpages.

Transitioning to COSMIC's new files

The COSMIC team wants to lead by example in encouraging data to be FAIR (Findable, Accessible, Interoperable and Reusable) compliant, and as part of this goal, they will be phasing out their current files for COSMIC v100 in May 2024. This means that the current download files will be retired and only the new style files will be available to download. 

→ Learn more about COSMIC's new files and transition support here.

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