NEW YORK (GenomeWeb) – Thomson Reuters has launched a new product called the Clinical Genomics Toolkit that bundles curated content from relevant public repositories as well as the company's own proprietary databases and internally developed analytic algorithms, and makes it available to clinical laboratories to help them better annotate and interpret clinically actionable variants identified by their tests and make useful therapy recommendations.
This is first product that Thomson Reuters has launched that is tailored specifically for use in precision medicine, Chris McKenna, the firm's general manager of discovery services, told GenomeWeb. The company has historically curated and sold content to support research and development activities in the pharmaceutical and biotechnology industry. But, according to McKenna, it sensed an opportunity to bring its data curation capabilities to bear on the genomic data interpretation market where dropping sequencing costs have resulted in larger datasets and further elucidated the links between genes, diseases, and drugs.
Currently, the system contains information on variants associated with oncology but Thomson Reuters is adding content that will support tests for variants associated with rare and inherited diseases. There's already some information available in the toolkit on genetic disorders, but Thomson Reuters plans to add more next year and then move on to other diseases. It's also planning to release a cleaner and more integrated version of the Clinical Genomics Toolkit next spring that will provide access to all the content and algorithms via a single API rather than multiple APIs which it has done the past, McKenna said. That release will include integration improvements to the toolkit's API to support VCF file processing and will introduce additional pathogenicity analytics currently under development, he said.
The Clinical Genomics Toolkit collates information from the public domain as well as from the company's own internal databases and makes it available for use by researchers and clinicians in commercial and academic pathology labs, as well as diagnostics companies that offer gene panels, whole-genome, and whole-exome sequencing-based tests. Clients who avail themselves of the toolkit will gain access to content from clinical guidelines and trials, peer-reviewed journals, and curated information gleaned from public repositories such as ClinVar, COSMIC, and dbSNP. The information is combined with drug content from Thomson Reuters' Integrity database, and interaction and pathway data from MetaCore, which the company acquired when it bought GeneGo in 2010.
These resources provide access to data on genomic variants and their associations to disease and drug response; biological pathways implicated in disease; actively recruiting clinical trials including patient inclusion and exclusion criteria; and investigational and marketed drugs and their associations with known genes.
Moreover, clients will be able to use analytics capabilities developed and offered by Thomson Reuters as part of the toolkit for predicting variant pathogenicity. This includes algorithms for disease similarity and genomic neighborhood scoring which could help users re-classify variants of unknown significance as well as classify newly discovered variants. McKenna said that Thomson Reuters is currently working with unnamed academic partners to develop additional algorithms for the system that will support tasks such as exploring variants in the context for biological pathways as well as connections to potential treatments, McKenna said.
Thomson Reuters intends to reach molecular testing labs by working with existing vendors of interpretation platforms and services to include the resource in their products and offer it as a supplementary source of information and analytics to their customers, McKenna told GenomeWeb. Labs that use vendors that partner with Thomson Reuters to include the toolkit in their systems would have the option to license, for undisclosed fees, the additional content offered by Clinical Genomics Toolkit.
The company is actively seeking vendors interested in incorporating its content and algorithms into their systems. It's already made an early access version of the toolkit available on the cloud-based platform offered by Cambridge, Mass.-based GenoSpace, one of the members of Thomson Reuters' so-called Life Sciences Partner Ecosystem. In fact, the Clinical Genomics Toolkit has its roots in an early partnership between the companies that dates back to when GenoSpace first joined Thomson Reuters' program in 2012. At that time, the partners discussed plans to develop an integrated offering to analyze and interpret human genomic variation and said that they would start with variants for cancer. Those efforts led to what is now being launched as the Clinical Genomics Toolkit. It is now part of GenoSpace's Fullview, a tool that lets users integrate results from multiple genomic and other diagnostic assays and compare them to various public and proprietary reference content as part of the interpretation process.
Thomson Reuters is also talking with a number of soon-to-be-named partners about a potential integration of its toolkit with their respective solutions, he said. The agreement with these vendors is set up such that customers deal directly with Thomson Reuters and not the data interpretation software vendors to gain access to the clinical content, McKenna said.
In addition to partnering with commercial interpretation providers, Thomson Reuters has an option to license its clinical content directly to testing labs that have developed and run their own bespoke annotation and interpretation pipelines internally. These sorts of customers have the option to integrate the Clinical Genomics Toolkit directly into the backend of their existing infrastructure or they can implement both the toolkit and an interface developed by Thomson Reuters called the Clinical Genomics Advisor to access both the content and analytics contained in the system. In either case, the company will provide services to support these customers, McKenna said.
In a bid to differentiate itself from competitors, Thomson Reuters focused on the quality of its content as well as providing a breadth of information on variants, biomarkers, and drugs it provides through the toolkit, McKenna said. The company has also put in place definitions and criteria to ensure that its system captures relevant information and presents it in a fashion that is meaningful to pathologists and clinicians as well as a mechanism for updating the database as new content becomes available, he added.