COSMIC Cancer Gene Census: Expanding Our Understanding of Human Cancers' Genetic Mutations

This blog post is a collaborative effort between Helen Speedy COSMIC and Denise Carvalho-Silva Open Targets, who can be reached at [email protected] for inquiries.

We are excited to share insights about navigating the complexity of cancer genetics through COSMIC, the world's most extensive resource cataloging cancers' somatic mutations. In our latest update from November 2018, COSMIC encompasses over 5.9 million coding mutations across more than one million samples, which have been meticulously curated from scientific literature and cancer-related databases like TCGA and ICGC.

Beyond just data, the suite of tools and datasets includes COSMIC-3D and the Cancer Gene Census CGC. The CGC is a pivotal resource that systematically compiles genes causally linked to cancers. Our QA below with Denise Carvalho-Silva sheds light on its ms, criteria for gene inclusion, recent expansion, hallmarks of cancer application, and user interactions.

Denise began by asking about the m of the Cancer Gene Census:

What is the overarching goal of the Cancer Gene Census?

The primary objective of the CGC is to systematically compile all genes that have a causal role in cancers. Initiated in 2004, today it features information on 723 genes.

When deciding which cancer genes to include, how do you evaluate them?

The decision-making process involves two key lines of evidence:

1 Evaluating COSMIC data for typical mutation patterns characteristic of a gene – for instance, frequent inactivating mutations in tumor suppressor genes versus missense mutations or indels in oncogenes.

2 Conducting an exhaustive literature review to understand the functional role of each potential CGC gene within cancer biology.

A significant recent enhancement was the introduction of two tiers - Tier 1 and Tier 2 - for assigning genes based on evidence strength:

Which criteria define a gene as being added to Tier 1 versus Tier 2 in the Cancer Gene Census?

For inclusion in Tier 1, we require:

• Two indepent publications demonstrating functional involvement in cancer hallmarks

• Two indepent publications reporting somatic mutations across at least one type of cancer

Genes that meet only these criteria are assigned to Tier 2.

But it doesn't stop there. We continuously update the CGC through new publications.

Why is this tier system important?

This systematic approach helps organize and prioritize genes based on their evidence strength, providing researchers with clear guidelines for their role in driving cancer biology.

Denise also inquired about using hallmarks of cancer for gene assessment:

How are hallmarks of cancer utilized within the Cancer Gene Census?

Identifying patterns in a gene's function that could facilitate drug design to target specific biological pathways or find effective combinations agnst different oncogenic processes is fundamental.

Moreover, our data offers insights into gene function, accessible both on the COSMIC website and through Open Targets Platform.

For more information, refer to our review published last month in Nature Reviews Cancer titled The COSMIC Cancer Gene Census: describing genetic dysfunction across all cancers.

This comprehensive Review discusses the 2018 Catalogue of Somatic Mutations in Cancer COSMIC Cancer Gene Census, an expert-curated catalog that recently expanded its scope to cover genetic dysfunctions in various cancer types.

If you're interested in this resource further and wish to provide new gene candidates for evaluation, feel free to contact us via eml. We welcome contributions from our user community.

We hope this gives a glimpse into the extensive use of COSMIC and CGC in advancing our understanding of cancer genetics. Stay tuned for more updates and insights!

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