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.
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.
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.
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.
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.
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.
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.
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:
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.
Read the statistics sheet.
Next-generation sequencing (NGS) has transformed the field of oncology. Early successes in identifying and targeting oncogenic drivers of solid tumors have set the foundation for genomics guided precision medicine; but, for hematological malignancies, the path to precision medicine is a lot more complex.
Within the hematologic oncology space, there is a spectrum of biologically related, but clinically heterogeneous diseases. In part, the differences between patients are driven by the particular combination of genetic mutations each disease acquires during its evolution. To effectively treat and manage myeloid malignancies, hematologist oncologists need highly parallel, highly sensitive assays that (1) enable the simultaneous analysis of multiple genes and (2) are coupled with indication-specific bioinformatic pipelines that provide information on disease classification, prognostication, treatment selection, and monitoring.
In this application note, we discuss the importance of streamlined clinical NGS workflows within the hematologic-oncology space. Learn how to develop a robust, automated, and streamlined NGS analysis pipeline for the interpretation and reporting of genomic alterations associated with hematological malignancies.
Read and download the application note >
Wednesday, March 25, hear from Dr. Anthony M Magliocco, CEO and Founder of Protean BioDiagnostics, as he discusses the application of whole exome sequencing for guiding clinical trial enrollment for patients with cancer.
The remarkable advances in precision medicine are unfortunately not currently available to all patients, especially those being treated in community cancer settings. This growing “gap” is now challenging the health system to provide cost-effective, scalable, innovative solutions for underserved patients. Protean BioDiagnostics was founded to close this gap and accelerate access to precision oncology for all patients, regardless of where they live. To this end, Protean has created an adaptable and innovative framework for rapidly deploying the latest companion diagnostics. Protean’s simplification of universal access to complex diagnostics is poised to change the practice of precision oncology in the community and truly “close the gap.”
In this webinar, you will learn more about
Date: Wednesday, March 25, 2020
Time: 11 am EDT
On April 22, Nature Medicine published the first results from the UK's TARGET (Tumor chARacterisation to Guide Experimental Targeted therapy) study. The letter, written by researchers funded by Cancer Research UK, The Christie Charity, AstraZeneca, and the NIHR Manchester Biomedical Research Centre (BRC), adds new evidence for the feasibility and potential utility of liquid biopsy to identify clinically actionable mutations and guide clinical trial enrollment for patients with advanced cancer.
Currently, enrollment to trials depends on a patient's type of cancer or genetic data obtained from an invasive tumor biopsy, which is often months or years old and may not represent a patient's current disease due to the tumor's evolutionary changes.
TARGET is a molecular profiling program with the primary aim to match patients with different types of advanced cancers to early phase clinical trials on the basis of analysis of both somatic mutations and copy number alterations across a 641 cancer-associated-gene panel in a single ctDNA assay. In the first of the two-part trial, the investigators were able to collect, process and analyze blood samples from 100 patients in the Manchester area.
The results show that a small volume of blood can contain up-to-date genetic information about a patient's cancer to inform treatment choices. In this feasibility study of the first 100 patients, 11 were molecularly matched and enrolled into an available therapy.
Investigators used QIAGEN Clinical Insight (QCI) to identify the clinically actionable variants and geographically available clinical trials, stating:
Functional annotation of somatic variants was performed using ANNOVAR, the resultant VCF file was analyzed through the QIAGEN Clinical Insight for Somatic Cancer platform and reports were generated for discussion in the TARGET Molecular Tumor Board. ‘Actionable’ was defined as a target of known pathogenic significance for which either a licensed or experimental agent or relevant clinical trial was available at the time of discussion.
The investigators go on to describe the importance of using clinical interpretation and reporting tools that are connected to comprehensive knowledge resources needed to minimize the number of variants of unknown significance (VUS) with evidence. As they explain, it is nearly impossible for tumor boards to have knowledge of every actionable variant:
A potential reason why large molecular screening programs have traditionally allocated only 10–15% of patients to studies may be in the interpretation of variants of unknown significance7,8,9. It is challenging for any MTB to have knowledge of all possible variants, and databases are in development for pooling relevance of variants of unknown significance23,24. We addressed this issue by accessing software packages to aid interpretation of the relevance of specific variants and to identify appropriate trials in different regions of the United Kingdom or Europe. The QIAGEN Clinical Interface software package was considered valuable in differentiating actionable mutations (and recommended matched therapies) from those of unlikely clinical relevance, and provided tiering following ACMG/AMP/CAP guidelines.
The researchers now hope the second part of TARGET, which is already underway, will show how often the blood test is successful at matching patients to early phase clinical trials and the impact this has on their overall survival. There is also an option of referring patients to other clinical trial sites, if suitable matched trials are available in other parts of the country--another great feature of QCI.
Reference: *Rothwell, et al. Utility of ctDNA to support patient selection for early phase clinical trials: The TARGET Study. Nature Medicine. (2019) DOI: https://doi.org/10.1038/s41591-019-0380-z
At the beginning of 2019, QIAGEN announced the acquisition of N-of-One, Inc., a molecular oncology decision support company that provides case-specific, expert-powered clinical NGS interpretation services and solutions.
We sat down with Sean Scott, QIAGEN’s Chief Business Officer and Vice President of Business Development for Clinical Genomics and Bioinformatics, to discuss QIAGEN’s plans for post-acquisition incorporation and what new value QIAGEN customers can expect.
How does the acquisition of N-of-One fit into QIAGEN’s clinical bioinformatics strategy?
Sean Scott: This acquisition represents a unique opportunity for QIAGEN and N-of-One to combine respective strengths to deliver the industry’s most robust portfolio of molecular oncology decision support solutions from one provider. N-of-One’s technology-enabled, yet human-driven, services and the proprietary MarkerMine™ database are planned to be integrated into QIAGEN Clinical Insight (QCI), our platform for NGS analysis and interpretation. We are opening the door to real-world evidence (RWE) and creating new opportunities for supporting healthcare providers and payers.
What does the acquisition mean from a pharmaceutical company’s perspective?
Sean Scott: The addition of N-of-One’s MarkerMine database and commercial data rights creates an attractive and expandable link into RWE insights. N-of-One’s Genomic Insights and analytics services can be commercialized to pharmaceutical industry partners—in particular to more than 25 companies with which QIAGEN has deep companion diagnostic co-development relationships—to support patient cohort analytics, patient stratification, trial protocol design, assay design and interpretation, trial accrual and market forecasting, patient-to-trial matching and other features.
How does N-of-One differ from other molecular decision support providers?
Sean Scott: N-of-One is one of the best-known brands in molecular oncology decision support. It is well-established with labs, pharma companies, and payers, and N-of-One has been the solution-of-choice for leading diagnostic companies, such as Foundation Medicine. Unlike other providers, N-of-One employs a team of over 30 PhD scientists and oncologists to research and analyze each patient case, and in the process, N-of-One has amassed one of the most comprehensive resources of oncology clinical and scientific evidence in the industry with more than 125,000 anonymized patient samples.
How could real-world evidence and patient data impact clinical development program design?
Sean Scott: Today, all stakeholders in the healthcare spectrum—pharmaceutical developers, payers, regulators, physicians and patients—are putting their money on the collection and analysis of many different types of RWE as a key enabling strategy, to close critical gaps in knowledge, give physicians and patients broader access to therapies, and help payers realize the actual value of those therapies in improving health and reducing costs. While still at an early stage, RWE is becoming increasingly used to complement traditional RCT data to inform important healthcare decisions. This suggests that RWE will have a significant impact on the healthcare industry in the years to come.
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Day One kicked-off with numerous informational sessions, including talks on the role of AI in clinical decision-making, the importance of standardization for reimbursement, and the tremendous potential of genomic profiling in disease prevention, diagnosis, and treatment.
Dan Richards, Vice President of Biomedical Informatics at QIAGEN, spoke about the clinician's current challenge of curating all the evidence he or she needs to confidently sign-off on variant reports before they go to the prescribing physician. QIAGEN Clinical Insight (QCI) and N-of-One were featured as solutions providing options for either in-house curation with tailored workflows or on-demand curation services.
On Tuesday morning, the conversation continued with a panel hosted by Sean Scott, Chief Business Officer of Clinical Genomics and Bioinformatics at QIAGEN, that discussed the emergence and application of real-world evidence in the clinical setting, especially in precision diagnostics and clinical trial protocol design.
The panel consisted of Raju K Pillai, MD, Hematopathologist and Molecular Pathologist at City of Hope National Medical Center, James Hadfield, Director and Principal Diagnostic Scientist at AstraZeneca, and Sheryl Krevsky Elkin, Chief Scientific Officer of N-of-One.
Also on Tuesday morning, Mary Napier, Associate Director of NGS Strategy at QIAGEN, gave a timely talk on how diagnostic labs and pharma companies can gain a comprehensive understanding of tumor mutational burden signature by implementing our new QIAseq Tumor Mutational Burden panel.
What does she mean by "comprehensive"?
Find out here!
Thank you to everyone who visited the QIAGEN booth, we truly enjoyed talking to all of you about the industry challenges, and changes you see happening now and in the future.
See you at our next event:
Advances in Genome Biology and Technology (AGBT) 2019 in Marco Island, Florida!
February 27th - March 2nd
Want to know more about our clinical solutions and real-world evidence?
Today, at the 60th Annual Meeting of the American Society of Hematology (ASH) in San Diego, California, QIAGEN announced the launch of two novel products to deliver actionable insights on a wide range of blood cancers: a new workflow for the QCI Interpret bioinformatics solution for hematological malignancies, and the new QIAact Myeloid DNA UMI Panel for use in myeloid neoplasm research as a Sample to Insight workflow on QIAGEN's GeneReader NGS System.
Meet and talk with our experts at ASH 18, booth #1557!
Featured Products and Solutions
Check out this recent article by American Health Leader (AHL) on how QIAGEN is helping clinical diagnostic and pathology labs adopt genomics-guided precision medicine workflows.
Sean P. Scott, Chief Business Officer and Vice President of Clinical Market Development at QIAGEN, explains QIAGEN’s holistic approach to developing and expanding NGS-based test services. “No matter the size of the lab, we’re focused on helping them understand how to develop a more insightful and actionable report for the ordering physician . . .”
Read the full article here!
QCI Interpret makes precision medicine possible by offering one, cloud-based platform to handle a range of genomic testing, from somatic to germline, from small panels to exome and whole genome.
Get in touch with one of our QCI Interpret experts today!
If you answered yes, we invite you to watch a free recording of our webinar that addresses one of the key bottlenecks of today’s clinical testing laboratory: producing standardized interpretation that is consistent among personnel, reproducible within the testing community, and in accordance with professional guidelines. We show how our clinical NGS reporting and interpretation software, QCI Interpret, not only makes precision medicine possible, but simplifies workflows and increases productivity.
We are proud to share an article written by Ramon Felciano, Chief Technology Officer and Vice President, Strategy & Technology, QIAGEN Bioinformatics, that was featured in The Pathologist, a UK-based publication that considers the latest research and innovation in pathology and diagnostics. Titled “Deciding Factors,” the article shines a light on new trends in clinical labs that are improving the accuracy and efficiency of genetic test interpretation. It argues that these advances are made possible with clinical decision support (CDS) tools, which incorporate big data, sophisticated informatics, and augmented intelligence (as opposed to artificial intelligence), to better inform treatment decisions, manage liability risk, and ensure compliance with ever-changing data privacy regulations.
The adoption and implementation of CDS tools is no longer a luxury, but rather a necessity. Just a few years ago in the United States, only pre-eminent academic medical centers offered precision medicine. As stated in the article, “Today, an estimated 24 percent of hospitals will provide some form of precision medicine by the end of 2018.”(1) With the use of CDS tools and related technologies gaining traction, clinical teams need to ensure they select support tools that provide maximum interpretation transparency and detailed reporting. Dr. Felciano explains how CDS tools are personnel assets—not replacements—that enhance productivity, reliability and the practice of precision medicine.
(1)N. Versel, “Data requirements, money hold back growth of precision medicine among health systems” (2018). Available at: https://bit.ly/2qFSb60. Accessed April 18, 2018.
