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AbbVie, Biogen, Pfizer Join With Broad Institute on Genebass Exome Variant Project

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CHICAGO – Three major biopharmaceutical companies have joined with the Broad Institute to create what they called the world's largest browsable resource linking rare protein-coding genetic variants to human health and disease. 

The portal, called Genebass, is a collaboration among AbbVie, Biogen, and Pfizer primarily intended to accelerate the completion of analysis of the entire UK Biobank exomic dataset, started three years ago by the UK Biobank Exome Sequencing Consortium. All three pharma firms are part of that consortium.

The three-year-old UK Biobank Exome Sequencing Consortium involves eight biopharmaceutical companies, including AbbVie, Biogen, and Pfizer. Nature Genetics recently published initial results of sequencing of 200,643 of the approximately 500,000 biobank enrollees, including around 10 million exonic variants.

Wade Davis, global head of computational biology at AbbVie's Genomics Research Center, said in an email that UK Biobank provided the Exome Sequencing Consortium with access to its samples for whole-exome sequencing and subsequent analyses. Genebass grew out of those analyses.

"The end goal was to develop a world-class portal to explore the results from the whole-exome sequencing association analyses that encompass both single-variant analyses as well as set-based analyses to understand gene-phenotype relationships," Davis wrote. "To get there, we wanted to use the same vetted processes that underlie trusted resources such as GnomAD," the Genome Aggregation Database.

Melissa Miller, director of human genetics at Pfizer, said that the Exome Sequencing Consortium released this preliminary data because participants were eager to get the information out to the research community.

The Exome Sequencing Consortium funded the generation of exome data from 500,000 UK Biobank participants, while Genebass is working on processing the data from the Exome Sequencing Consortium.

According to Biogen, while UK Biobank is not directly participating in Genebass, the organization has approved all data processing associated with Genebass. "They have been a great collaboration partner in discussing both the setup of infrastructure as well as how it should be best released to the public," the biotech firm said in an email.

Biogen provided written answers to questions from GenomeWeb without attributing the comments to a specific person.

Miller said that the pharma partners came up with Genebass because they were looking for a way to make the UK Biobank exome data more useful and accessible for their own researchers. "We knew we wanted to build some sort of visualization tool so that use of the data wasn't just limited to geneticists," she said.

Miller, who holds a Ph.D. in genetic epidemiology, said that the competitors went into Genebass as equal partners. UK Biobank provided the data but did not take an active role in the creation of Genebass.

"In the case of the UK Biobank [exome data], that's a large enough effort that it makes sense to bring multiple companies together to be able to complete that," Miller said.

"We believed working together to develop an intuitive user interface to showcase the analysis results was the best path forward. It would also accelerate getting to the competitive part of the process, which is selecting target-indication pairs and developing treatments based on that," said Davis.

Pfizer, Biogen, and AbbVie tapped the Broad Institute to process the data and conduct association testing on close to 4,000 phenotypes from the UK Biobank in hopes of finding associations between specific genes or variants and diseases. Results will be made publicly available through the Genebass portal.

The Broad Institute is bearing the computational "heavy lifting," as well as helping to coordinate Genebass work, according to Miller. "They're really the ones that have the infrastructure in place to handle a large dataset like this," she said.

"By combining the expertise of the healthcare industry and the nonprofit research community, we can carefully assess how biomedical data at this unprecedented scale is best utilized and hopefully accelerate the path from genetic discoveries towards novel therapeutics," Anthony Philippakis, the chief data officer of the Broad Institute, said in a statement.

Biogen identified five goals for the three pharma partners in Genebass: harmonization and quality control of the exome data; quality control of the UK Biobank phenotypes; linking genetic and phenotypic data through exome-based association analysis; creation of a browser; and development of a platform for continued use and processing of the exome data.

The company said that it will primarily use Genebass data to identify new drug targets and to validate new and existing hypotheses from human data.

"We hope this dataset will be used broadly by scientists across disciplines, both in academia and industry, to advance the science around the link between rare protein-coding genetic variants to human health and disease," Biogen said.

Miller said that Pfizer is interested in exome sequencing as a way to identify genetic variants that have significant effects on certain traits or diseases. "Those larger effect sizes can give you an idea of potential therapeutics you might be interested in," she said.

Pfizer also wanted to be a part of the Genebass project because looking at this much data can be "pretty daunting to know where to start." Her group at Pfizer wanted more than just geneticists examining the data, both within and outside the company, and Genebass makes the datasets more accessible.

"We're really excited to see what kinds of discoveries that other people make in using the tool as well," Miller said. She said it was "fun" on the date Genebass was released to see the general research community post findings on Twitter from their initial searches of the resource.

"What we're really looking forward to the most is getting as many eyes on the data and seeing what other people discover," Miller added.

According to Davis, Genebass is targeted at any scientists who want to improve their understanding of the biology of the human genome. "There are relatively few labs in the world with access to such high-quality information, and Genebass makes that freely available to anyone with a web browser," he said.

Davis added that the partners are "open to where Genebass may take us and committed to its ongoing success," including through inviting others to participate.

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