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Startup BioSkryb Eyes Oncology Applications for Single-Cell DNA Sequencing

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NEW YORK – A North Carolina startup is hoping to take genomic research to the single-cell level, with a new whole-genome amplification technology.

"I haven't done bulk RNA sequencing in probably five years," said Charles Gawad, cofounder of Durham, North Carolina-based BioSkryb (pronounced "bio-scribe") and a professor at Stanford University Medical School. "The richness of data is so much deeper. We can do the same thing for DNA."

BioSkryb is launching a line of sample preparation kits based on primary template-directed amplification (PTA) chemistry. The firm has exclusively licensed the patent-pending IP from St. Jude Children's Research Hospital, where Gawad developed it to research cancer genetic heterogeneity. The proprietary flavor of PTA, called SkrybAmp, offers up to 99 percent genome coverage and variant call rates of up to 90 percent at 30x coverage, Gawad said. For comparison, a 2017 study of whole-genome amplification (WGA) methods used in single-cell exome sequencing, from researchers at Sweden's Science for Life Laboratory, found that Ampli1 technology, an MDA-based approach, led to about 10 percent of variants called; while multiple annealing and looping-based amplification (MALBAC), another non-MDA method, led to 16 percent of variants called.

SkrybAmp chemistry is flexible, Gawad added, allowing for copy number and structural variant detection. "We can enrich for and capture any fraction of the genome we want," he said.

BioSkryb plans to initially go after the niche market of labs running MDA for single-cell DNA analysis with its SkrybAmp Single-Cell Kit, which will run 96 cells following fluorescence-activated cell sorting, CEO and Cofounder Jay West said.

Ultimately, the firm hopes to attract new people to the field. "We're really interested in enabling new discoveries," Gawad said. "Panels, by definition, are using targets you already know are important. We want people to discover new mutations and alterations that are not known." Beyond discovery, BioSkryb also has plans to make single-cell DNA sequencing a part of clinical practice.

Gawad got his start with single-cell DNA sequencing in 2012, when he joined the Stanford lab of single-cell sequencing pioneer Stephen Quake. "The challenge with DNA was the quality of the data you got," with MDA methods, Gawad said. "It was not sufficient to answer the biological questions we wanted to address."

MDA is plagued by a so-called "jackpotting effect," he explained. "Where you get priming, that part takes off and you cover a lot." His idea to resist that was to slow down the reaction speed with nucleotides designed to terminate products between 200 bases and a couple kilobases, so the regions that did not initially get priming could catch up.

Gawad started his own lab in 2015 at St. Jude's and used PTA to tackle questions about cancer heterogeneity. But he believed the WGA technology could prove powerful in several other areas where genomic differences between cells was important, including CRISPR off-target analysis, non-invasive preimplantation genetic diagnosis, rare disease diagnosis, and even microbiome research. After filing for patents in January 2018, he began talking with West, a former Fluidigm senior director of R&D, later that year. They cofounded BioSkryb in August 2018 and have linked up with private equity firm Anzu Partners, who led their $11.5 million seed funding round, announced earlier this month.

BioSkryb has 10 employees on site in Durham, with another 10 to 15 contractors. Anzu offers companies in its portfolio some services, including finance and human resources. Anzu's David Michael said his firm does this "to make it easier to scale. And it has worked well." 

West said that BioSkryb has made "additional improvements" to PTA "with additional patents pending," but declined to discuss them. Gawad added that he felt SkrybAmp could be pushed to get even more variant calls and because it uses direct ligation, and barcodes could be incorporated into the products to increase throughput.

The SkrybAmp single-cell kit will be the company's first product, for use in the sequencing workflow ahead of standard library preparation. "We believe our library outputs are compatible with the range of sequencing technologies," West said, but the kit is configured for use with Illumina's platforms. The firm will also launch accessories to improve kit performance, such as magnetic plate technology to help with purification and bead cleanup kits.

With a 30-minute hands-on time and a thermal cycler as the only necessary equipment, SkrybAmp can compete with MDA or MALBAC for use in single-cell DNA sequencing, the firm said. "That's our most easily addressable market," Gawad said.

BioSkryb has begun disseminating SkrybAmp to about 15 key opinion leaders. The firm said participants signed confidentiality agreements and that none were able to discuss their experience with the single-cell kit. "Once we get data back, which we have, we'll begin an early-access program that is going to start quite soon," offering a 24-cell version of the kit, West said. "Definitely within the next month or two."

The single-cell DNA analysis market is small, with just a few companies offering either kits or platforms. Commercialized MDA-based WGA methods include Qiagen's Repli-g, Silicon Biosystems' Ampli1 WGA, and Rubicon Genomics' PicoPlex DNA-seq and Picoseq. 10x Genomics offers a Single-Cell CNV solution based on its Chromium system. And Mission Bio offers droplet-based, high-throughput, single-cell DNA analysis through its Tapestri platform.

But West said BioSkryb is "fundamentally different" from Mission Bio. "They're running targeted panels. We analyze the entire genome."

"In terms of our ability to create single-cell exomes, we don't really have a lot of competition. We're going to have an unfair advantage in this market space," he said.

That market space could one day include clinical applications, if the team's vision for SkrybAmp comes true.

"Cancer is much more complex than people realize," Gawad said. "Now we have the tools to detail that complexity. Our longer-term vision is those discoveries be useful clinically."

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