The accurate identification and annotation of germline and somatic variants rely on the accuracy and depth of reference databases that contain information about the genetic variants, any associated phenotype, and their clinical implications. By combining COSMIC, HGMD and QIAGEN QCI-IT, scientists can annotate gene variants using the world’s most comprehensive and up-to-date curated scientific evidence and find biological connections in gene variants with manually curated scientific findings. The software and databases allow you to get valuable and reliable insights for your research project and speed up your discoveries related to disease-causing and disease-associated germline and somatic variants.

In this training, you will:
1. Learn about COSMIC, the world’s largest, most comprehensive, expert-curated resource for somatic mutations in human cancers, and how COSMIC can help you identify variants of interest for cancer research.
2. Hear about the breadth and depth of HGMD (Human Gene Mutation Database) and how HGMD can aid in your search for disease-causing and disease-associated germline mutations.
3. Explore the capabilities of QCI-IT, which can help accelerate your discoveries from hereditary or tumor cohort analyses, and find associations between gene variants and diseases from VCF files.

To learn more about the products or request for a trial:

COSMIC: https://digitalinsights.qiagen.com/products-overview/cosmic/?cmpid=CM_QDI_DISC_042024webinars

HGMD: https://digitalinsights.qiagen.com/products-overview/clinical-insights-portfolio/human-gene-mutation-database/?cmpid=CM_QDI_DISC_042024webinars

QCI-IT: https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/qci-interpret-translational/?cmpid=CM_QDI_DISC_042024webinars

How expert-curated cancer data from COSMIC and HSMD can help biopharmaceutical researchers identify and validate targets faster and optimize clinical trial design.

In cancer drug discovery and development, data is king. From identifying potential molecular targets to helping predict drug toxicity and optimizing clinical trial design, high-quality data can significantly improve the efficiency and success rate of bringing new cancer therapies to market.

The Catalogue Of Somatic Mutations In Cancer (COSMIC) and the Human Somatic Mutation Database (HSMD) are two expert-curated somatic databases exclusively licensed through QIAGEN that enable biopharmaceutical researchers to avoid pitfalls in early cancer drug discovery, confidently qualify candidate drug targets, and accelerate indication expansion and repurposing of existing cancer therapies.

In this blog, we take a closer look at COSMIC and HSMD for biopharmaceutical research, providing an overview of the expert curation processes, what types of data can be found in each database, and examples of how this data can be applied through the cancer drug discovery and development pipeline.

How COSMIC's cancer data supports oncology drug discovery

COSMIC is an expert-curated knowledge base providing data on somatic variants in cancer, supported by a comprehensive suite of tools for interpreting genomic data, discerning the impact of somatic alterations on disease, and facilitating translational research. The catalogue is accessed and used by thousands of cancer and biopharmaceutical researchers and clinicians daily, allowing them to quickly access information from an immense pool of data curated from over 29 thousand scientific publications and large studies.

COSMIC integrates somatic data from multiple sources published around the world and allows researchers to access and scrutinize information about somatic mutations and their impact in cancer. Over the past two decades, COSMIC has been diligently collecting, cleaning, and organizing genomic data and associated metadata from cancer studies published in scientific literature and various bioinformatics sources. This data is then translated into a standardized format, integrated, and made available to the research community through well-structured datasets and user-friendly data exploration websites and tools.

In addition to the main catalogue of somatic mutations, a further 6 accompanying resources focus on different aspects of oncology (Figure 1). The Cancer Gene Census (CGC)  and Cancer Mutation Census (CMC) provide additional annotations regarding the roles of genes and mutations in oncogenesis, which are based on a defined set of rules and sufficient evidence obtained through dedicated literature curation and analysis of the content of the core catalogue.

→ View the complete database numbers in the latest COSMIC v99 (December 2023) here.

Figure 1. COSMIC’s 7 key resources for understanding cancer and improving cancer patient care. The main catalogue of somatic mutations is supported by further six resources that together lay additional layers of knowledge helping to interpret the impact of somatic mutations on cancer development and presenting available therapeutic options (graphic from Sondka et al. 2024).

COSMIC's expert curation process

COSMIC’s workflows to manually curate cancer genetic data have been built to deliver high-quality, biologically and clinically-relevant data to the research community. Different data sources and types of curated data require different approaches (Figure 2). However, in each case there are common core elements.

• Firstly, the source of the information is identified from the peer reviewed literature or bioinformatic resources, and checked for the quality and relevance of the content.

• To enable meaningful analysis by end users, data need to be adequately and transparently categorized. This is achieved by combining the use of controlled vocabularies that label data and a database schema that is able to represent these vocabularies.

• Before data extraction, all curated features and terms are converted to vocabularies, ontologies and data conventions used by COSMIC. Genes, variants, and transcripts use external vocabularies and ontologies. For interoperability, all COSMIC disease classifications have been mapped to the NCI thesaurus ontology and these mappings can be downloaded from the COSMIC website.

• Acquiring the data itself is the final stage of curation.The minimum unit of curation is: a genetic variant, tumour type and the scope of the study, i.e. which genes were tested. In addition, whenever reported by the publication, other clinical features for the patient are curated e.g. age, gender, ethnicity, therapeutic history, family history of cancer or exposure to DNA-damaging agents. At the tumour level, the curation team extracts information on cancer stage and grade, metastases, drug response and therapy relationship, i.e. if a sample was collected prior to, during, or post-therapy.

Figure 2. COSMIC data curation flowchart. Depending on the data source and curation objectives, there are three main curation paths in COSMIC (graphic from Sondka et al. 2024).

How HSMD's cancer data supports oncology drug development

HSMD is a web-based application that allows biopharmaceutical researchers and clinical NGS testing labs to harness genetic insights from QIAGEN’s real-world oncology dataset combined with knowledge from two decades of expert curation.

In the latest version of HSMD, the resource focuses on providing deep insight into small variants, such as SNVs, indels, frameshifts, fusions and copy number variants that have been clinically observed or curated from scientific literature to help users better understand and define precise function and actionability. This expert-curated resource contains content from over 547,000 real-world clinical oncology cases combined with content from the QIAGEN Knowledge Base (QKB), providing gene-level, alteration-level, and disease-level information.

HSMD enables users to easily search and explore mutational characteristics across genes, synthesize key findings from drug labels, clinical trials, and professional guidelines, and receive detailed annotations for each observed variant (Figure 3).

Figure 3. HSMD home screen. HSMD enables users to search by gene, alteration, disease, drugs, and clinical trials.

HSMD's expert curation process

HSMD leverages variant content from two sources: expert-curated content from the QIAGEN Knowledge Base (QKB) and data from real-world oncology cases sourced from our professional clinical interpretation services (Figure 4).

When a variant has been “clinically observed,” it means our professional clinical interpretation service has encountered this alteration in a real-world clinical case. For these variants, QIAGEN's team has assessed the clinical and biological relevance and  calculated the gene and variant prevalence across observed tumor types. Conversely, content from the QKB is proactively curated from scientific literature; therefore, not all variants have yet been directly clinically observed by our professional clinical interpretation services.

Figure 4. HSMD curation workflow. HSMD contains content from the QKB, which pulls information from all public and proprietary databases, clinical articles for the most relevant cancer genes, and thousands of clinical articles for somatic genes. Curation then occurs by artificial intelligence (AI) approaches, manual curation, or a combination of both. All content then goes through rigorous quality control to ensure consistency, accuracy, and reproducibility. In addition, HSMD contains content from over 500,000 somatic mutations submitted to QIAGEN's professional variant interpretation service, QCI Precision Insights (formerly N-of-One). This is de-identified patient data that provides even greater insight into real-world clinical cases.

Trusted cancer data to accelerate drug discovery and development

COSMIC and HSMD are two expert-curated databases licensed exclusively through QIAGEN that enable biopharmaceutical companies to improve the drug discovery process, develop more effective clinical trials, and enhance the treatment of rare cancers. To learn more about how your research team can use COSMIC and HSMD, visit our product webpage or click the button below for a free trial and personal consultation with our biopharmaceutical research experts.

COSMIC & HSMD FOR BIOPHARMA


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Want to learn more?

Read an expert article on how biopharma researchers can use genomic knowledge bases to bring better drugs to more patients in less time.

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In this case study, learn how biopharmaceutical companies can use HSMD to identify potential new indications for existing cancer therapies.

DOWNLOAD CASE STUDY

Two expert-curated databases exclusively licensed through QIAGEN link sequence-level somatic mutation data to detailed molecular information about functional and clinical impacts, as well as implications for druggability and relevant clinical trials. The two databases, the Catalogue Of Somatic Mutations In Cancer (COSMIC) and the Human Somatic Mutation Database (HSMD), enable biopharmaceutical researchers to avoid pitfalls in early cancer drug discovery and development, confidently qualify candidate drug targets, and accelerate indication expansion and repurposing of existing cancer therapies.

In this blog, learn more about the high-level applications of using COSMIC and HSMD in cancer drug discovery and development pipelines.

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The Catalogue of Somatic Mutations in Cancer (COSMIC)

The Catalogue Of Somatic Mutations In Cancer (COSMIC) is the most detailed and comprehensive resource for exploring the effect of somatic mutations in human cancer. Developed and maintained by Wellcome Sanger Institute, the latest release, COSMIC v99 (December 2023), includes over 6 million coding mutations across 1.5 million tumor samples, curated from over 29,000 publications. In addition to coding mutations, COSMIC covers all the genetic mechanisms by which somatic mutations promote cancer, including non-coding mutations, gene fusions, copy-number variants and drug-resistance mutations.

COSMIC integrates somatic data from multiple sources published around the world and allows researchers to access and scrutinize information about somatic mutations and their impact in cancer. Over the past two decades, COSMIC, through predominantly manual curation workflows, has been diligently collecting, cleaning, and organizing genomic data and associated metadata from cancer studies published in scientific literature and various bioinformatics sources. This data is then translated into a standardized format, integrated, and made available to the research community through well-structured datasets and user-friendly data exploration websites and tools.

The Human Somatic Mutation Database (HSMD)

The Human Somatic Mutation Database (HSMD) is a relatively new somatic mutation database from QIAGEN (released in 2019) that combines over two decades of expert curation and data from scientific literature, on- and off-label therapies and clinical trials, and real-world clinical oncology cases. In the latest release, HSMD 3.0 (November 2023), the database contains manually curated, detailed molecular information on over 1.8 million somatic variants, with more than 430,000 observed in real clinical cases, as well as data from over 545,000 real-world clinical oncology cases.

Unique to HSMD is the availability of data from clinically observed variants. When a variant has been “clinically observed,” it means QIAGEN’s professional clinical interpretation service (previously N-of-One) has encountered this alteration in a real-world clinical case. For these variants, QIAGEN assesses the clinical and biological relevance and calculates the gene and variant prevalence across observed tumor types.

Easy to search with new content added weekly, HSMD enables researchers to explore key genes or mutations with driving properties or clinical relevance and search for associated treatment options, off-label therapies, resistance markers, and regional and/or disease-specific clinical trials.

Applications of COSMIC and HSMD in cancer drug discovery and development

While similar, COSMIC and HSMD differ in their applications for cancer drug discovery and development. As a result, biopharmaceutical researchers can use both databases to support different workflow stages.

How COSMIC supports exploratory research in cancer drug discovery

COSMIC is a valuable resource for cancer researchers and drug discovery efforts. Here are several ways in which the COSMIC database can be used to support exploratory research in cancer drug discovery:

• Identification of mutations in target genes - COSMIC provides a comprehensive catalog of somatic mutations observed in various cancer types. Researchers can use COSMIC to identify mutations occurring in the gene associated with the drug target. Evaluating the prevalence and distribution of mutations can help assess the potential impact on the function of the target.

• Frequency of mutations across cancer types - Analyzing COSMIC data allows researchers to assess the frequency of mutations in the target gene across different cancer types. Higher mutation frequencies in specific cancer types may indicate the relevance of the target in those cancers, supporting its potential as a drug target.

• Correlation with clinical data - COSMIC integrates clinical data, including patient outcomes. Researchers can correlate mutations in the target gene with clinical parameters such as patient survival, response to treatment, or disease progression. Positive correlations may suggest the potential significance of the target in predicting clinical outcomes.

• Functional impact of mutations - COSMIC provides information on the functional impact of specific mutations. Understanding whether mutations in the target gene are driver mutations (contributing to cancer development) or passenger mutations (incidental changes) is crucial. Driver mutations are more likely to validate the target as a potential therapeutic intervention.

• Validation across datasets - Researchers can cross-validate findings from COSMIC by comparing them with data from other sources, such as The Cancer Genome Atlas (TCGA) or other cancer genomics databases. Consistency across multiple datasets strengthens the validity of the target.

• Exploration of drug response data - COSMIC includes data on drug response, allowing researchers to explore how cancer cell lines with specific mutations in the target gene respond to different drugs. Assessing drug response data helps predict potential therapeutic strategies and identifies drugs that may be effective against cancers with specific mutations in the target.

• Integration with pathway analysis - COSMIC provides information on pathways associated with mutated genes. Researchers can integrate this data with pathway analysis tools to understand the broader biological context of the target. Pathway analysis helps identify potential interactions and dependencies that can further validate the significance of the target.

How HSMD supports cancer drug clinical development and post-market research

HSMD is a valuable resource for biopharmaceutical researchers, facilitating the confident evaluation of cancer-related genetic variations by granting access to real-world data. Here are several ways in which HSMD supports cancer drug clinical development and post-market research.

• Identify clinical function of somatic mutations - HSMD enables researchers to easily search and explore mutational characteristics across genes, synthesize key findings from drug labels, clinical trials, and professional guidelines, and receive detailed annotations for each observed variant.

• Conduct research use only (RUO) studies - Researchers can leverage HSMD to deepen their understanding of disease mechanisms at the molecular level. RUO studies can explore how specific genetic alterations contribute to disease initiation, progression, and resistance, providing insights into potential therapeutic interventions.

• Clinical trial optimization – HSMD contribute significantly to clinical trial optimization by facilitating patient recruitment, informing trial design, and providing valuable insights throughout the trial lifecycle.
  • Patient stratification – The real-world, de-identified patient data in HSMD enables the identification of eligible patients based on specific criteria for clinical trials. Improved patient identification streamlines recruitment efforts, accelerates trial enrollment, and reduces the time and costs associated with the initiation phase.

• • Clinical trial feasibility assessment – With clinical trial data that can be segmented by geographic location, HSMD can used to assess the feasibility of conducting a clinical trial at specific sites or within particular patient populations. Understanding patient demographics, disease prevalence, and historical treatment patterns aids in identifying suitable trial locations and estimating recruitment potential.

• • Regulatory submission and approval – HSMD data can complement traditional clinical trial data in regulatory submissions, providing additional evidence of a treatment's effectiveness and safety. Regulatory agencies increasingly recognize the value of real-world evidence in supporting decision-making during drug approval processes.

• • Companion diagnostic design – Users can search HSMD by disease and receive a ranked list of associated genes to help design custom assays that enable better prediction of response and resistance to specific therapies.

• Drug repurposing - HSMD enables the analysis of the frequency and distribution of somatic mutations across various cancer types. The database also provides a catalog of drugs employed in the treatment of patients with specific mutations, along with available response data. Using this information, researchers can explore potential new indications for existing cancer drugs.

Transform targets into precision cancer therapies

COSMIC and HSMD are two expert-curated databases licensed exclusively through QIAGEN that enable biopharmaceutical companies to improve the drug discovery process, develop more effective clinical trials, and enhance the treatment of rare cancers. To learn more about how your research team can use COSMIC and HSMD, visit our product webpage or click the button below for a free trial and personal consultation with our biopharmaceutical research experts.

COSMIC & HSMD FOR BIOPHARMA


REQUEST FREE TRIAL

Want to learn more?

Read an expert article on how biopharma researchers can use genomic knowledge bases to bring better drugs to more patients in less time.

READ ARTICLE

In this case study, learn how biopharmaceutical companies can use HSMD to identify potential new indications for existing cancer therapies.

DOWNLOAD CASE STUDY

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.

(more…)

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.

(more…)

• Explore the wide range of datasets that COSMIC offers, including the Cancer Mutation Census and Mutational Signatures;
• Gain insights from COSMIC’s gold standard genomic data by taking either a disease or gene centric view of your research;
• Identify potential applications of COSMIC data and how it enables users from a plethora of disciplines to experiment and innovate with confidence.

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 the demand for precision oncology increases, so does the need for a comprehensive cancer genomic knowledge base. Here are 5 reasons why you should be using COSMIC for biopharmaceutical research.

1. Guaranteed precision through expert curation

Precision is crucial in developing biopharmaceuticals. Unlike other somatic databases, COSMIC is meticulously and rigorously curated by a team of highly trained, PhD-level experts. This manual curation—the gold standard in genomic curation—ensures that every data point undergoes human scrutiny, giving scientists unparalleled confidence in the accuracy and consistency of the data they rely on. Through comprehensive literature searches, COSMIC’s experts have curated, standardized, and cataloged mutation data, phenotype information, and clinical details from over 1.5 million cancer samples and 29,000 peer-reviewed papers to date.

2. Unrivaled transparency for trustworthy insights

COSMIC provides an unmatched level of traceability for every data point, empowering scientists with transparency and fostering confidence in the presented evidence. With COSMIC, there is no 'black box'; each piece of information can be traced back to its source, providing users with complete visibility into its origins. This complete transparency is invaluable for biopharmaceutical scientists, especially when dealing with rare variants or variants of unknown significance. In these cases, users can independently assess each piece of data, exercising their judgment on whether to agree or disagree with COSMIC’s data for a particular variant.

3. Bridging the drug discovery gap

In the pursuit of precision oncology, biopharmaceutical scientists must address a wide range of questions about somatic alterations as druggable targets. COSMIC stands as the largest repository of comprehensive genomic, phenotypic, and mutational characteristics of cancers. With COSMIC, you can obtain the most exhaustive information available on mutations associated with a specific cancer type, the frequency and tumor distribution of a specific alteration, driver oncogenic events, candidate therapeutic targets, and much more.

Furthermore, COSMIC’s Actionability functionality assists scientists in tracking and exploring drugs in various stages of development, monitoring the progress of clinical trials, and investigating drugs repurposed to target specific mutations.

And unlike other databases relying on volunteers, COSMIC is continually updated by its team of dedicated expert scientists, ensuring you have access to the accurate and up-to-date insights necessary to advance your translational research efforts.

4. Versatility in data manipulation for enhanced insights

In the dynamic field of biopharmaceuticals, adaptability is essential. COSMIC offers exceptional flexibility, enabling users to customize their data mining, visualization, and manipulation processes. COSMIC can be seamlessly integrated into your IT systems, allowing automatic updates or scheduled integration of newly released datasets to align with your individual workflow. COSMIC also allows you to customize filters according to your pipeline and fully integrate its data with proprietary databases to obtain a single comprehensive view. With COSMIC, you can easily align the data precisely with your unique research processes, enhancing your ability to extract actionable insights.

5. Trust, credibility, and global adoption

In biopharmaceutical research, credibility is earned through adoption. Over 50,000 molecular pathology labs, clinicians, bioinformaticians, and researchers worldwide trust and use COSMIC. It has also been cited in over 10,000 publications. Its extensive usage attests to its accuracy, consistency, and reliability. Recognized in the AMP/ASCO/CAP guidelines as a foundational evidence source for somatic variant assessments, COSMIC allows biopharmaceutical scientists to align their work with the highest standards in the field.

How to try COSMIC 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.

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

COSMIC Actionability's latest release brings 5 new fully curated somatic genes, 948 new clinical trials, and more

We are pleased to announce the availability of a new release for COSMIC, the Catalogue of Somatic Mutations in Cancer. COSMIC Actionability v9 adds new actionability data to the world’s largest, expert-curated somatic mutation database. The release includes 5 new fully curated somatic genes, 948 new clinical trials, and 100 new oncology drugs.

In this article, we provide a summary of the COSMIC Actionability v9 release highlights.

What is COSMIC?

COSMIC, the Catalogue of Somatic Mutations in Cancer, is an expert-curated database encompassing the wide variety of somatic mutation mechanisms causing human cancer. Owned and maintained by the Wellcome Sanger Institute, COSMIC is exclusively licensed through QIAGEN.

COSMIC’s team of variant scientists manually curates key cancer genes to provide in-depth information on mutation distributions and effects. The team relies on a semi-automated curation process of cancer genomes to provide broad somatic annotations toward target discovery and identification of patterns and signatures. To date, COSMIC contains nearly 24 million somatic mutations associated with human cancers.

What is COSMIC Actionability?

COSMIC Actionability is a standalone product within the COSMIC database that focuses on providing information on the availability and development of drugs targeting somatic mutations in cancer. COSMIC’s certified curation team integrates data from case studies, clinical trials, and regulatory bodies to represent a full picture of the current precision oncology pipeline (from drug development, through safety and clinical phases, to market and repurposing).

Actionability contains information on three core units: mutations, diseases and drugs. By capturing relations between these units, COSMIC’s team identifies existing and upcoming drugs that target specific genetic variants in different cancer types.  COSMIC Actionability is a cutting-edge, ‘living-tool’ that provides the most up-to-date data for precision oncology applications.

What’s new in COSMIC Actionability v9?

• 5 additional fully curated genes: ESR1, CCND1, CCND2, CCND3 and RB1
  
• 948 new clinical trials:  COSMIC Actionability now contains 4,610 trials with results and 5,746 trials with no results—that's a total of 10,356 clinical trials!
• 100 new drugs: COSMIC Actionability now contains 1,835 drugs.
• 72 new somatic variants: With the new release, COSMIC Actionability now contains 876 total somatic variants.

→ View the full Actionability v9 release notes here.

Want to know more about COSMIC?

Learn more about COSMIC and how the industry-leading database can help you identify biomarkers, annotate variants, and explore the etiology of human cancers here.

Download COSMIC sample data

See first-hand how COSMIC can be used in your lab by downloading sample data here.

• Delve into our manual curation and rigorous data annotation processes, and how the resulting gold standard data enables users to experiment and innovate with confidence.
• Gain insight into the motivations behind our curation focuses and the results of our latest focus: rare skin tumors, including new tumor types/histologies, a newly fully curated cancer gene and more.
• Explore the revamped COSMIC download files, with particular focus on their interoperability, accessibility and useability.