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With Biobase Buy, Qiagen Adds 'Critical' Data Layer to Bioinformatics Portfolio


NEW YORK (GenomeWeb) – Continuing the bioinformatics buying spree it began last year, Qiagen has acquired German biological data provider Biobase, renamed Qiagen Wolfenbüttel, for an undisclosed sum and has begun integrating some of Biobase's curated repositories with the bioinformatics assets that it gained when it bought Ingenuity and CLC Bio.

For example, it has begun merging the information on inherited mutations and genes that affect drug response, which are contained in Biobase's Human Gene Mutation Database (HGMD) and its PharmacoGenomic Mutation Database (PGMD), respectively, into Ingenuity Knowledge Base, the genetic data repository that underlies the entire Ingenuity product line.

Data from HGMD is already available to Ingenuity Variant Analysis customers — HGMD is also integrated with the CLC Genomics Workbench — and the company is working on other integrations that will be available later, according to Doug Bassett, chief scientific officer and chief technology officer for Qiagen Silicon Valley, which was formerly Qiagen Redwood City and before that was called Ingenuity. Biobase's data will also support Ingenuity Clinical, a new web-based clinical NGS interpretation and reporting solution currently being tested by teams at Partners Healthcare, Emory Genetics Laboratory, GeneDx, and other laboratories.

As Qiagen Wolfenbüttel, Biobase will continue to provide free standalone versions of its databases to academia and to license standalone versions to industry — its prices remain the same. It's an approach to business that has been "very successful in engaging and enabling the community," Bassett said. On the one hand, it provided a budget-friendly option for clients with smaller purses and at the same time supplied the revenue needed to keep the business running. "It delivers value to the community … [and] it's our intent to continue that model," he said. That’s good news for companies such as Cypher Genomics which licensed GenomeTrax, Biobase's repository of pathogenic variants, in 2012 for use in its NGS analysis services business. On the academic front, Biobase's clients include the Luxembourg Center for Systems Biomedicine, which began using Genome Trax in 2012 to analyze next-generation sequencing data for use in clinical diagnostics.

With Biobase, Qiagen believes it can provide the most comprehensive biomedical content on the market to support next-generation sequencing-based studies and tests."This merger allows us to deliver fundamentally enhanced customer value in NGS interpretation and enhances the Qiagen bioinformatics ecosystem with some great offerings like HGMD that help our customers get from sample to insight faster," Bassett told BioInform. Qiagen opted to purchase Biobase instead of simply taking advantage of its licensing scheme because it believed that ownership made the most sense in terms of providing the best support for customers and growing Qiagen's informatics business more generally. "NGS interpretation is fundamentally powered by … content and so making sure we've got the right, high-quality, highly structured, comprehensive content in place is a critical piece of the puzzle for us," he said.

Moreover, pooling the efforts of curators and bioinformaticists from both companies "allows us to cover the biomedical literature in a more comprehensive way than ever before," he said. "We can … curate a much larger corpus of articles with a higher capacity and deliver more customer value with really high-quality, highly structured content solutions." Working together will also help to eliminate redundancy in the curated resources, Bassett added. There are cases where having multiple groups curate the same article has value in terms of ensuring the accuracy and quality of the curation, he said. "Going forward, we can actually manage that redundancy of curation such that we are optimizing the coverage of the literature corpus."

Furthermore, the acquisition brings in new business for Qiagen's informatics unit. "We were impressed to see that there is relatively small overlap in our customer bases … for the informatics solutions," Bassett said. "There are a lot of cases, for example, where proteomics labs are using Qiagen's Ingenuity Pathway Analysis solution for pathway analysis and interpretation and would really benefit from … the Biobase products. We are in a position to combine, bundle, integrate, and connect resources like that so the customer gets the most combined benefit."

In fact, as a sort of celebration of the acquisition, customers who currently use either Biobase's HGMD but have not tried Qiagen's Ingenuity Variant Analysis and vice versa will receive a free trial of whichever solution they have not used before. This way, they get to see "the power of using the products and the content solutions to analyze and interpret their data together instead of separately," Bassett said.

Bassett declined to comment directly on whether or not Qiagen has plans to purchase additional informatics assets but he did say that the company is keeping an open mind. "We are always on the lookout for collaborations and opportunities that can maintain our leadership in bioinformatics" and focused on providing "collaborative content and data interpretation resources for customers who are working with NGS data," he said. "This [involves] a pretty complex array of build-versus-buy decisions that will unfold over time but the Biobase merger is a key piece of the puzzle in ensuring that we've got the right content capabilities and curation capacity and bioinformatics talent in place to drive forward this market."

Furthermore, Bassett said, as the company launches the Ingenuity Clinical product and future capabilities, it will increasingly enable decision support and interpretation of sequence-based tests. Other opportunities for product integrations within the Qiagen bioinformatics ecosystem could include providing customers of Ingenuity Pathway Analysis with connections and links to Biobase products that they are also licensing, he said. "We wanted to focus that first release on the integration that's actually here today and delivering customer benefit … but we do have other integrations and capabilities that we'll be talking about in the months to come."

Biobase was founded in 1997, is based in Wolfenbüttel, Germany, and has more than 600 customers in the pharmaceutical industry and academia. Its roughly 100 employees have all joined Qiagen and will continue to operate out of company headquarters in Germany and branch offices in the US, India, and Japan. Michael Tysiak, Biobase's CEO is now the general manager of Qiagen Wolfenbüttel.

In addition to HGMD, PGMD, and Genome Trax, Biobase also created and maintains the Transcription Factor Binding Sites database, which contains information on eukaryotic transcription factors and miRNAs; Proteome, which contains data on genes and miRNAs; and BRENDA, a collection of enzyme functional data among other resources. In late 2012, the company signed an agreement with the University of Southern California and the Children's Hospital of Pennsylvania that allowed it to commercialize and distribute Annotate Variation — more commonly known as ANNOVAR — an open source software tool for annotating genomic variants. Qiagen has no immediate plans to retire or consolidate any of the existing Biobase products.