COSMIC, the Catalogue Of Somatic Mutations In Cancer, is the world's largest and most comprehensive resource for exploring the impact of somatic mutations in human cancer. When it was created in 2004 by researchers with the Cancer Genome Project in conjunction with the Sanger Institute, COSMIC was set up with a big ambition–to be the source of all cancer genomic knowledge.

Today, COSMIC contains nearly 24 million genomic variants across 6,800 precise forms of human cancer. It is the most expansive, expert-curated knowledge hub available for somatic NGS data analysis and interpretation. From molecular pathologists matching mutations to targeted therapies to bioinformaticians looking for patterns of DNA mutations in cancer cells, COSMIC is an excellent resource for identifying and understanding cancer mutations.

Now, as genomic testing of cancer moves into routine clinical practice, the need for a comprehensive knowledge base is even greater. Here are 5 reasons why your clinical lab should be using COSMIC.

1. You can be confident in the accuracy and consistency of the data

Unlike other genomic databases for cancer, COSMIC is manually curated. A team of highly trained, PhD-level experts perform exhaustive literature searches to curate, reorganize, interpret, standardize, and catalog mutation data, phenotype information, and clinical details. To date, information from over 1.5 million cancer samples and 29,000 peer-reviewed papers have been systematically entered into COSMIC.

Why is this value to molecular pathology labs?

Nothing can replace human judgment. While machine learning and artificial intelligence may help in the speed of data collection, these digital systems do not (yet) have the capability to reconcile differences in terminology, determine whether the results of the studies are statistically valid and relevant, or translate the information in a paper to a standardized ontology framework. Manual curation is the gold standard. When you use COSMIC, you can be confident your data has already passed through the “eyes” of another expert.

2. You can trace every data point to the direct source

In COSMIC, every data point is traceable to the source, data processing is documented, and the user has full control over all the data. The data organization structure is fully transparent. All of the data sources that contribute to COSMIC’s ability to help molecular pathologists characterize cancer samples and mutations, such as peer-reviewed papers, genome-wide screen data, and cancer cell line omics data, can be reviewed via direct evidence source references.

 Why is this value to molecular pathology labs?

There is no “black box” in COSMIC. Users can trust the data being presented because COSMIC allows users to review the evidence for themselves. This is particularly valuable when molecular pathology labs encounter rare variants or variants of unknown significance. In these cases, the user can exercise their judgment on whether to agree with or disagree with COSMIC’s data for that particular variant.

3. You can match drugs to cancer mutations

In March 2021, COSMIC revealed a new functionality—called Actionability—that allows users to search drugs that target somatic mutations at all stages of drug development, including those still in development, in clinical trials, or that have been repurposed.

Why is this value to molecular pathology labs?

When it comes to analyzing and interpreting somatic NGS tests for precision oncology applications, molecular pathology labs need to answer 3 key questions: which mutations a tumor needs to survive, which drugs can target those mutations, and which treatment is best suited for the genetic profile of the patient’s cancer.

While COSMIC isn’t the only database trying to provide these links between mutations and drugs, it is one of the few with a dedicated, full-time team of scientists keeping it updated. While others tend to be maintained by volunteers in the cancer research community or collated through crowdsourcing (which can yield unreliable, inconsistent data), COSMIC regularly monitors literature and drug labels, adds evidence from case studies and abstracts to describe emerging druggable biomarkers, and adds evidence on new genes.

4. You can customize how you mine, visualize and manipulate the data

COSMIC is designed to provide ease-of-use and maximum flexibility. Users have full control of how they search the data, visualize the data, and manipulate the data for specific panels and/or pipelines. You can integrate the complete raw dataset into your lab’s proprietary database.

Why is this value to molecular pathology labs?

Having easy and ready access to data and evidence is vital for molecular pathology labs analyzing and interpreting somatic NGS tests for precision oncology applications. COSMIC can be fully integrated into your IT system to automatically update. The database also allows you to customize filters according to your pipeline and merge data tables to have one, comprehensive view.

5. You can trust the quality of COSMIC

If you are still unsure about using COSMIC after the aforementioned reasons, don’t take our word for it—look at who else is using COSMIC. More than 50,000 molecular pathology labs, clinicians, bioinformaticians, and researchers worldwide use COSMIC. To date, COSMIC has been cited over 10,000 times in peer-reviewed articles.

Why is this value to molecular pathology labs?

There’s a reason why COSMIC is so popular among the clinical NGS community. The data is accurate, consistent, up-to-date, and highly recommended as a foundational evidence database for somatic variant classifications. In fact, COSMIC is listed in the AMP/ASCO/CAP guidelines as an Evidence Source for the clinical assessment of somatic variants [1]. If integrated, COSMIC enables molecular pathology labs to adhere to accurate, standardized variant interpretations.

How to try COSMIC in your lab today

Trying COSMIC in your lab is easy. Simply visit the official COSMIC website, scroll to the bottom of the page, and "Request A Demo". One of our experts will contact you immediately about scheduling a free demo of COSMIC using your lab's data.

Have questions? Want to know more? Check out our COSMIC resource hub here.

References:

1. Li MM, Datto M, Duncavage EJ, et al. Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. J Mol Diagn. 2017;19(1):4-23. doi:10.1016/j.jmoldx.2016.10.002

In oncology research, identifying potentially actionable gene alterations and exploiting cancer’s molecular vulnerabilities is becoming increasingly difficult. Due to the sporadic nature of somatic cancers, the number of variants detected is rapidly rising.

Clinical research labs are tasked with confidently identifying meaningful mutations that could influence or improve decisions at the point of care. To do this, they need ready-access to trusted data to validate biomarkers and better assess their biological and clinical relevance. And this is precisely what the Human Somatic Mutation Database (HSMD) provides.

HSMD can be used to:

1. Gain insights from real-world data and two decades of expert curation: HSMD’s oncology dataset combines manually-curated content from the QIAGEN Knowledge Base─the industry’s largest collection of biological and clinical findings─with data from over 419,000 real-world clinical oncology cases that have been analyzed and interpreted by QIAGEN’s professional clinical interpretation service. With HSMD, researchers don't need to collect information manually across different knowledge bases and resources.
2. Quickly classify VUS’ and controversial variants: Labs sometimes risk of over-interpreting variants of unknown significance (VUS), which could lead to unnecessary or potentially harmful treatments. When you encounter a variant with limited information, you can use HSMD to look for observed clinical case distribution, biochemical impact, functional impact, and actionability.
3. Analyze complex genetic reports: Molecular tissue profiling often generates difficult-to-interpret genomic information─making the resulting reports either too complex or lacking in data on the clinical actionability of detected variants. HSMD can be used to rapidly drill down to variant-level information, derive actionable data from complex reports and evaluate clinical impact.
4. Stay up to date: HSMD’s content is updated weekly, so labs can ensure that variant interpretation reports are based on the most relevant and timely evidence. Over 5,000 manually curated alterations are added to it each month.
5. Establish an in-house bioinformatics pipeline: HSMD can be used to develop an in-house pipeline to help manual variant curation. Using HSMD, labs can annotate a single variant in under 15 minutes. Ordinarily, manually curating one variant can take an experienced curator 3-4 hours to complete. Depending on the size of the panel, a single VCF file can contain thousands of variants to annotate. This requires the lab to search for available data online and query population databases and gene-and/or locus-specific databases to perform in silico analysis, evaluate the literature, analyze functional studies, and find clinical trials and relevant therapies.

HSMD 2.0 comes with over 140,000 new alterations, improved data visualization and new structural variants. The dataset now contains over 419,000 clinical oncology cases and over 1.5 million mutations associated with over 4.2 million relationships from PubMed, drug labels, clinical trials, clinical guidelines and public databases such as gnomAD and HGMD.

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