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Qiagen Brings Clinical Variant Interpretation, Reporting Software to Market


This article has been updated to correct Sean Scott's position at Qiagen.

NEW YORK (GenomeWeb) – Last week, Qiagen announced the commercial launch of Qiagen Clinical Insight, a content and software platform that provides clinical testing laboratories with tools to interpret and report on genomic variants from next-generation sequencing based tests.

The platform helps clinical researchers evaluate genomic variants in the context of published biomedical literature, professional association guidelines, publicly available databases and annotations, drug labels, and clinical trials. It offers tools for classifying variants, identifying potential treatment options, and matching patients to clinical trials located near them. Initial applications for the platform are for somatic and hereditary cancer testing.

Qiagen acquired the system that is now the Clinical Insights platform when it purchased Ingenuity — now Qiagen Redwood City — in 2013. Ingenuity had been developing the product for some time prior to the acquisition in collaboration with partners such as the Laboratory Corporation of America, Life Technologies (now Thermo Fisher Scientific), and GeneInsight, a wholly owned subsidiary of Partners HealthCare.

Laura Furmanski, the head of Qiagen's bioinformatics business area, said in a statement that in creating the platform, the company gathered input from more than 100 clinical testing laboratories and then worked with 50 of those labs to use the software and content contained in the platform in their workflows for laboratory-developed tests. In addition to LabCorp and GeneInsight, the company worked with major cancer centers such as Memorial Sloane Kettering Cancer Center, Emory Genetics labs, molecular pathology labs, and others to gain clarity on the unmet needs and challenges of molecular diagnostics and NGS-based testing, Sean Scott, vice president of clinical genomics at Qiagen bioinformatics, told GenomeWeb in an email.

He said partner labs provided feedback on things like methods of managing scientific complexity, appropriate mechanisms for scaling test offering, and the need for comprehensive literature support and genomic reference datasets. Partners also highlighted the importance of support for germline and somatic cancer variants, expected standards for clinical evidence and methods of presenting information to clinical labs, and the importance of cross-platform and workflow support for various test indications.

One of those collaborators was Gregory Tsongalis, the director of the molecular pathology and translational research program at the Dartmouth-Hitchcock Medical Center. In a statement, Tsongalis noted that getting from raw sequence data to clinically actionable variants and reporting those variants in a user-friendly format that ordering physicians can make sense of continues to be a "significant challenge" for molecular testing labs.

"Working in collaboration with Qiagen on the development and validation of the Clinical Insight platform in support of somatic cancer testing has resulted in scalable and reproducible results in addressing our labs unmet bioinformatics needs and challenges," he said.

Tsongalis told GenomeWeb this week that as part of the evaluation process, his lab used Clinical Insights to analyze numerous VCF files generated from a 50-gene cancer hotspot panel. He said in an email that his group liked the speed of the platform but had some suggestions that ultimately improved the way information was presented in the clinical report to make it easier to peruse.

Qiagen initially intended to release the solution commercially last year following an early access program and a beta in early 2014. It's not clear why the release was delayed but the company said it has spent the intervening years honing and improving the software prior to last week's full launch. Among other tasks, they worked on "optimizing" the tool's clinical content curation protocols to ensure that they comprehensively and accurately cover and represent the information available in scientific literature, drug labels, professional guidelines, and clinical trials, Qiagen's Scott said. The company also spent time developing and validating the support that the platform provides for the different workflows, frameworks, analytics, and reporting methods that are used to interpret and explore germline and somatic variants, he said. 

Qiagen's Clinical Insight platform could compete with solutions from companies such as Cypher Genomics, which recently launched an updated version of its Mantis software specifically for interpreting genetic variants in cancer applications. It will also have to contend with interpretation services vendors such as N-of-One and CollabRx. However, Qiagen believes its platform is a cut above the competition because it was developed and validated in collaboration with the primary target market, Scott said. Moreover the platform offers access to a comprehensive biomedical knowledgebase coupled with clinical evidence and genomic data pooling from resources such as the Qiagen-led Allele frequency community. The company also provides complete support for its annotation, interpretation, and reporting workflows, Scott said.