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Qiagen Q&A: how the COSMIC database is advancing precision oncology

By Darcy Jimenez 15 Apr 2021 (Last Updated May 10th, 2021 14:09)

Precision oncology offers a promising means of matching the most appropriate and effective treatments to individual cancer patients, but the vast amounts of genomic data it requires means the approach is not without its challenges. Qiagen’s Frank Schacherer and Beate Litzenburger discuss how the COSMIC database is enhancing cancer drug discovery, and the promise it holds for precision oncology.

Qiagen Q&A: how the COSMIC database is advancing precision oncology
Credit: Shutterstock

When it comes to cancer drug research, the ultimate goal is to find a treatment that has both high efficacy and minimal side effects. Precision oncology, which tailors therapies to the molecular characteristics of individual tumours, has emerged as means of matching the most appropriate and effective treatments to individual cancer patients, or specific sub-sets of broader treatment populations – but the approach is not without its challenges.

The heterogeneous nature of cancer means profiling tumours and developing targeted therapies for them is no small feat; to identify the gene mutations driving specific cancers, researchers need access to vast amounts of high-quality genetic mutation data. The more genomic information that is available, the better chance scientists have of identifying cancer predisposition genes and characterising the many molecular subtypes found in tumours – and this is where resources like the COSMIC database are invaluable.

The Wellcome Sanger Institute’s COSMIC (Catalogue of Somatic Mutations in Cancer) database is the world’s most extensive and comprehensive digital repository of somatic mutations in cancer. Licensing and distribution rights to the online resource, which has curated 10 million mutations to date, were acquired by life sciences research support firm Qiagen earlier this year.

Qiagen’s vice president of products and solutions Frank Schacherer and global product director for oncology Beate Litzenburger discuss why the COSMIC database appealed to the company, and the promise it holds for the future of cancer medicine.

Darcy Jimenez: How did this deal with the Wellcome Sanger Institute come about?

Frank Schacherer: There’s a bit of backstory; we have commercialised quite successfully several other academic knowledge assets before, the most well-known of those is probably the HGMD database, which is a database for hereditary mutations. I think Sanger was aware of our track record in this regard, and Sanger had already started to look for a way to secure sustainable funding for maintaining the COSMIC resource.

This is a very typical challenge when you start an academic research project; you need to maintain these databases, and you need ongoing funding for it to do all the curation. So, Sanger already had started in this direction, and then they realised that we have a lot more background and expertise in this field, and they could benefit from working with us to implement that.

DJ: In layman’s terms, can you describe the genetic cancer information that the COSMIC database contains, and how this can enhance drug discovery in oncology?

FS: COSMIC is the leading database for somatic mutation information. The kind of data COSMIC contains is a vast collection of known mutations from cancers, including annotations on those mutations, like how often they have been seen, what cancers they have been seen in, are they associated with certain treatments? Are they associated with certain outcomes? And I think COSMIC is unique in that it is by far the largest collection of such information. There are over 1,700 cancer types that are covered in there – there’s nobody else that covers such a wide range. They have over 37 million coding mutations that are stored in the database, and it is a very broad resource that enables biomarker research and discovery, as well as clinical testing workflows.

Beate Litzenburger: I think one of the other unique values is that it not only covers the mutations, but also everything that’s associated with a tumour sample. What it allows the pharmaceutical industry to do is take 1.5 million tumour samples, and because it’s a standardised database, start developing what they call virtual cohorts, divide them into groups of similar cases, and analyse differences between the different groups to determine if there’s anything that’s really, really specific about one of the groups – called a biomarker, or a specific signature. And that allows the pharmaceutical industry to then further dive into some of the specifics of what potentially drives tumours and the development of cancer.

DJ: Why did the COSMIC database appeal to Qiagen? In what ways is it valuable?

FS: Our entire brand is built around having premium, high-quality, manually curated content powering our solutions. COSMIC is the gold standard for somatic mutations in that regard – it’s a very high-quality, manually curated and maintained resource. There are over, I think, 10,000 times that the database has been cited in scientific literature, there are over 20,000 academic users of COSMIC, so it is a standard in the field.

We actually get approached quite often for commercialising academic software or academic products, but they need to have a level of acceptance in the community to make it worthwhile to commercialise them. And that is what attracted us to COSMIC, because we believe it is a unique resource and it is a widely accepted resource as a standard. There is a benefit in maintaining this resource for the benefit of the research community, and to secure this ongoing stream of funding to continue maintaining it.

DJ: To what extent will Qiagen work with the institute to further develop the COSMIC database and its capabilities?

FS: The fundamental arrangement is that the Sanger institute is creating the COSMIC database and we as their commercialisation partner are distributing the COSMIC database for commercial use. The database remains free to use for academic research use, but any commercial use – so like if you’re an academic testing centre, or you’re running a testing service for patients and so on, these kinds of commercial applications where you’re getting paid for it – they are being licensed by us. That’s the fundamental arrangement. However, as you can imagine, we have a lot of expertise also ourselves in curating data maintaining databases, so there may be in the future, extended collaborations where we work together to further improve the database. For non-academic, non-research users, at the moment, however, the relationship is to purely distribute, while Sanger creates and maintains.

DJ: Qiagen has an extensive portfolio of hereditary and somatic genetic mutation interpretation software and databases. What is the company’s overarching mission for these products, and how does the COSMIC database fit in?

FS: The overarching mission for Qiagen is to make improvements in life possible. The mission in this wider context for the informatics is to democratise access to knowledge and to bioinformatics analysis capabilities, by making them easy to use and easy to integrate into your workflow. We do have offerings that are really useful for bioinformatics experts or for data scientists, but the goal is to enable the researchers where the focus is not on the data wrangling only, but also on the scientific content, to enable them to directly interact with the data.

DJ: What potential does the database have for the future of precision medicine in oncology?

FS: I believe that COSMIC is one of the fundamental elements for any kind of precision medicine effort in somatic cancer. If you want to do precision medicine, you need to understand the right mutation, the right patient, the right treatment, all of the things matching together. And COSMIC has a lot of very finely curated data to make that possible, so I think it’s one of the foundational elements in developing a precision medicine-offering strategy or service.

DJ: Does the COSMIC database have strong competition in the market, in terms of datasets laying out the genetic drivers of human cancers?

FS: In general, I would say COSMIC is quite a unique resource in the scope that it has. COSMIC covers a wide range of information, so for specific elements of this, there are of course other offerings. Precision medicine is a large field, so there are a lot of other offerings that cover some of these partially – for example, cBioPortal gives you access to some cancer types, or there are more specific specialised databases on mutations. But I don’t think there’s any resource that really has the breadth and depth of content that COSMIC has, which made it attractive for us.

BL: I think COSMIC is by far the largest database that characterises human cancers, and that allows the researchers to capture more breadth and depth of data and do more complex analysis. Other databases that are used by the pharmaceutical industry are just not as large, and that basically hinders labs or companies coming up with bigger cohorts to do sample analysis.

So you have 1.5 million cancer samples in COSMIC, versus some of the other databases like The Cancer Genome Atlas or cBio, where you only have thousands of data points. And that makes a big difference for the pharmaceutical industry, which will ultimately need big data to come to conclusions. So, yes, there are other databases out there, but they don’t match the breadth and depth of the content in COSMIC – and that ultimately leads to greater insights into the genomics of tumours.

DJ: Qiagen is the Wellcome Sanger Institute’s first commercial partner. How do you plan to roll out the database to new commercial customers, and what has response been like in your early discussions with potential customers in the pharma and biotech space?

FS: Responses have been very positive; we have had a lot of traction already from engaging with our customer base. We just started with this, and there have already been multiple deals closed. Essentially, we have specialist sales teams that are already in conversation with these biotech and pharma companies because of our other offerings – we are present in basically all of the large pharma and biotech companies in the world with some of our offerings – so it is quite easy for them to include COSMIC in the conversation when we have a discussion about renewal of our other products, and so on. We have an active specialist sales team approach, which is quite important for COSMIC because it’s a very technical product. We have a very strong field application scientist team; these are scientists that can demonstrate use case or applications of the data, or answer questions of how you could leverage the database for answering the problem that you have. So they can work with the pharma customers to go through the use cases that the customer may have, and demonstrate how you could use COSMIC to address them.

I feel very honoured that Sanger chose us as their commercialisation partner; as you said, this is the first time Sanger ever did such a commercialisation. And I think it is a quite an achievement for an academic organisation like this to have this foresight and the willingness to explore a new modality – and it is very honouring that they saw a reliable partner in us, that would be able to be their counterpart. Sanger has a sterling reputation to protect, so they couldn’t have done this with just any partner.