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Bio-Rad Buys GnuBio; Will Focus on NGS-based Dx for Oncology, HLA, Infectious Disease

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Bio-Rad Laboratories said last week that it acquired next-generation sequencing technology firm GnuBio for an undisclosed price with the goal of commercializing a clinical NGS system.

GnuBio will remain based in Cambridge, Mass., where it is developing a droplet-based next-gen sequencing system that uses "picoinjector" technology developed in Co-founder David Weitz's physics laboratory at Harvard University.

Brad Crutchfield, president of Bio-Rad's life science group, told In Sequence that GnuBio will be integrated into Bio-Rad's Digital Biology Center. Bio-Rad formed its Digital Biology Center in 2012, shortly after it acquired QuantaLife in 2011, in order to develop an expertise around digital biology. Crutchfield described the center as a hybrid between the company's life sciences and diagnostics fields. GnuBio CEO and Co-founder John Boyce will head up the Cambridge location of Bio-Rad's Digital Biology Center.

While the GnuBio technology will continue to be developed at Bio-Rad's Digital Biology Center, it will be commercialized and sold through Bio-Rad's clinical diagnostics organization, Crutchfield said. "Our focus [with GnuBio] is very much targeted in developing a clinical analyzer," he said. "It's not a discovery tool at all."

Bio-Rad develops tools within the life sciences research and clinical diagnostics fields, including droplet digital PCR technology. According to Crutchfield, GnuBio's droplet-based sequencing platform will complement Bio-Rad's droplet digital PCR technology.

"We have an investment in the droplet digital technique and certainly have been successful with droplet digital PCR in establishing a paradigm and building a team in the area around droplets," Crutchfield said. "When we began to look at GnuBio, it became clear that we had some opportunities to expand the multiplexing capability that we have with our ddPCR system."

GnuBio "gives us the opportunity to get a much more multiplexed approach for a clinical diagnostics setting," he added.

GnuBio has been developing an NGS-based system with a focus on targeted sequencing applications for the clinical market. It began shipping systems to beta testers late last year and first showed the system and some initial data from 24 runs of a 36-gene panel at last year's Consumer Genetics Conference in Boston.

The technology works by first pipetting DNA into a cartridge, where it is sheared into 1-kilobase-sized fragments. The picoinjector injects the DNA into microdroplets that contain PCR primers representing the amplicon to be sequenced.

After enrichment, fluorescently labeled hexamers hybridize to the DNA fragments in the droplets and act as primers for DNA polymerase. According to GnuBio, the picoinjector technology enables 10,000 uniplex reactions per second, which enables the machine to use just 1/1,000th of the reagents required of other NGS systems.

Read length of the sequencing system is initially expected to be about 1 kbp, and GnuBio has previously said that it plans to develop targeted sequencing panels of up to 50 genes with the ability to detect alleles at frequencies down to five percent.

According to Crutchfield, Bio-Rad does not plan to introduce any fundamental changes to the technology, but will bring expertise around droplets and droplet technology to the development of the system. Additionally, Bio-Rad will help in bringing the system from a prototype instrument to one that can be manufactured at production scale.

In the past, GnuBio has said that it would sell its instrument for $50,000 with gene cartridge panels costing around $200, but Crutchfield said that it is too early to say how the system will be priced.

Crutchfield said that initial assays will be within the fields of oncology, HLA, and infectious diseases for clinical diagnostics. He said the company intends to seek regulatory clearance from the US Food and Drug Administration for both the instrument and the assays.

Currently, Illumina's MiSeqDx is the only next-gen sequencing system to have FDA 510(k) clearance. Crutchfield said that it was not yet clear whether Bio-Rad would have to submit a separate 510(k) application for the GnuBio system or whether it would be considered to have the same intended use as MiSeqDx and the company could instead self-register the system with the FDA. The self-registration process is more akin to Europe's CE marking process and only applies to similar technologies with the same "intended use."

For instance, Thermo Fisher's Life Technologies has said it does not need to go through the same 510(k) application process for its Ion Torrent PGM system as Illumina did for its MiSeqDx system since the PGM has the same intended use as the MiSeqDx. Instead, the company will go through a registration process by which it must demonstrate that the system meets certain guidelines and standards set by the FDA.

While the clearance of one next-gen system may pave the way for additional companies to gain FDA clearance of subsequent next-gen sequencing systems, it could also mean steeper competition in the clinical sequencing space.

However, Crutchfield said that the GnuBio sequencing system would occupy a different niche than the MiSeqDx due to its highly targeted nature. "It is very limited in scope," he said. GnuBio has so far reported data from a 36-gene panel and has said that its panels would include around 50 genes. "We don't look at this as a head-on [competitor] against Illumina."

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