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BGI Americas Banks on Chinese Institute's Vast Sequencing and Bioinformatics Capacity

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By Julia Karow

Five months after setting up shop in the US, BGI Americas is busy working with both customers and collaborators on more than 20 projects, as its Chinese mother institute is scaling up its sequencing and bioinformatics capacity in Hong Kong and Shenzhen.

Earlier this year, BGI, which is headquartered in Shenzhen, founded branches in Copenhagen and Cambridge, Mass., to serve as interfaces for customers and scientific collaborators in Europe and North, Central, and South America, respectively (IS 5/25/2010).

BGI Americas, formed in April as a for-profit US corporation, has grown to about 10 staffers, including bioinformaticians as well as sales representatives on the West Coast, New Jersey, and the Washington, DC, area.

"We have been busy," Paul Tu, president of BGI Americas, told In Sequence from China last week on the eve of an agreement of intent between BGI and Merck to collaborate in genomics-based research in the future (see other story, this issue).

Like its Chinese parent, BGI's US branch has taken a page from both an academic genome center and a for-profit sequencing service provider in that it conducts its own research, provides sequencing and bioinformatics for collaborative research projects, and offers fee-for-service work. Since the number of projects fluctuates constantly, it is impossible to say what percentage fall into each category, Tu said.

More than 20 customer and collaborative projects are currently ongoing, including academic researchers at scientific institutes and large US hospitals as well as pharmaceutical firms, none of which can be named yet. "If you name the big pharma, we work with them," Tu said.

Among the customers are Marcelo Menossi, a researcher at the University of Campinas in Brazil, as well as the National Institute of Diabetes and Digestive and Kidney Diseases, which said last month that it plans to award a project to sequence a single human genome to BGI (IS 8/3/2010).

Sequencing services run the gamut from de novo sequencing, whole-genome resequencing, exome sequencing, RNA sequencing, and epigenomic projects to microbial sequencing, and include humans, animals, plants, and microorganisms.

Customers and collaborators, who can submit projects of any size, can expect a fast turnaround time, extensive bioinformatics support, accurate data, and flexible collaboration models, Tu said. "We don't just do sequencing, we do value-added projects," he said.

But the institute also offers competitive pricing. According to Menossi, "price was a key point" in his decision to award an RNA-seq project to BGI.

Compared to other service providers, he said, BGI offered to do his project in "half the time, [for] half the price, including an improved bioinformatics analysis." He said he received back more reads than originally promised and found the overall quality of BGI's work — which included an in-depth bioinformatics analysis — to be "very good."

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Asked what BGI could improve, he said that it could provide more details on protocols, such as library construction, and on its bioinformatics tools, such as parameters and filters used. He also wishes for web-based software tools so customers can do their own analyses after receiving their data.

Because of the scale of its operations, BGI can dedicate entire instruments, as well as teams of bioinformaticians, to work with a specific collaborator or customer. This provides additional assurance that a partner's intellectual property is protected, an issue that Tu said BGI takes very seriously. "We don’t share anything with anybody in terms of new discoveries," he said. "As big as we are, and working on that many projects and working with that many customers, we don't breach their trust."

All sequencing work for international researchers is currently conducted at BGI's Hong Kong facility, which the institute built last year. The main reason for this offshoot from its Shenzhen headquarters is the ease of shipping samples internationally to Hong Kong, Tu explained, which is much easier than shipping to the mainland. "In terms of commerce, all the rules and regulations [in Hong Kong] are very similar to the US," he said, and even shipping clinical samples is "very routine." The facility is currently not able to provide regulated sequencing, but BGI plans to have the Hong Kong lab both CLIA-certified and CAP-accredited in the future.

By the end of the year, the Hong Kong location will be outfitted with at least 100 Illumina HiSeq 2000 machines — 65 were installed as of last week — as well as 20 Applied Biosystems SOLiD instruments, Tu said, adding that the number of SOLiDs might grow, "depending on the customer demand in human resequencing."

The Shenzhen facility will have 37 HiSeq 2000 instruments and between 5 and 10 SOLiD instruments and will focus on domestic sequencing projects, Tu said.

BGI is keeping an eye on new sequencing technologies as well, and "once they become more stable, and have proven they can scale, we will adopt them," Tu said. He added that the institute does not favor one vendor over another in deciding which platforms to adopt.

By the end of the year, BGI as a whole will have the capacity to generate an estimated 5 terabases worth of sequence data per day, equivalent to more than 50 human genomes at 30-fold coverage. Last year, the institute's capacity was only 100 gigabases per day, corresponding to three human genomes.

On the bioinformatics infrastructure side, the goal is to grow BGI's capacity to about one exabyte of storage and 50,000 CPUs by the end of this year, compared to 10 petabytes of storage and 5,000 CPUs at the end of 2009. The institute also provides several of its SOAP bioinformatics tools for next-gen sequencing data analysis on its website.

Tu said that at last count, BGI had 3,900 employees in total, 1,500 of them working in bioinformatics.

For BGI Americas, the current plan — subject to sufficient demand — is to build a US-based sequencing facility next year, which would "take advantage of the latest and the newest sequencing technologies," Tu said. The US facility would be mainly designed to handle small pilot projects with quick turnaround times for customers or partners, while larger projects would continue to be conducted in Hong Kong to leverage that center's scale and efficiency.

Part of the funding for BGI's current expansion comes from fee-for-service work, as any revenue BGI generates feeds back into the organization. In addition, the institute has a $1.5 billion credit line from the China Development Bank (IS 1/12/2010), which Tu said it leverages to support its operations and its expansion.

BGI Americas is not profitable yet, and receives funding from its parent for collaborative projects at the moment, but once it turns a profit, it will reinvest it into its own projects and collaborations as well, Tu said.

On its website, the US branch lists several of BGI's own initiatives, including a project to sequence the genomes of 1,000 plants and animals; a project to define the genetic basis of 1,000 Mendelian disorders by exome and whole-genome sequencing; a project to characterize mutations in complex diseases; and an RNA-seq project.

BGI Europe, located at the University of Copenhagen faculty of life sciences, follows the same model as its US counterpart, according to Bicheng Yang, a BGI spokesperson. The European branch plans to recruit five to 10 staffers over the next six months, and between 20 and 50 next year. BGI has said in the past that it also plans to open branches in Southeast Asia and Australia.

University of Campina's Menossi said he will definitely use BGI Americas' services again. In the past, he said, China has decreased the price of many consumer goods. "Now it seems that they are moving to more elaborate stuff, like sequencing [and] bioinformatics. I am sure this will have a worldwide positive impact."

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