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BGI Offers Next-Gen Sequencing Service, Kicks Off 100-Genome Sequencing Project

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With seven Illumina Genome Analyzers and two Applied Biosystems SOLiD systems in place, other new sequencing platforms under consideration, and a genome of a Chinese individual already sequenced, the Beijing Genomics Institute is staking its claim in next-generation sequencing, both as a commercial provider and in the research arena.
 
Last month, the private research institute said it has begun providing worldwide sequencing services on its Sanger and next-gen platforms. This week, BGI announced that is has signed on its first volunteer for the Yanhuang Project, a research effort to sequence at least 100 Chinese individuals.
 
With its debut in next-gen service work, BGI is potentially raising the stakes for other sequencing providers, including companies such as Agencourt Bioscience, SeqWright, Fasteris, and GATC Biotech.
 
The institute’s main competitive edge may lie in the cost of its services. “It will definitely be the most competitive price in the world,” Zhuo Li, vice president of BGI’s newly formed US subsidiary, BGI-USA, told In Sequence last week. “We will beat anybody.”
 
Li, who is also in charge of BGI’s worldwide international collaborations, did not disclose pricing information but said that BGI knows how much Illumina and a number of US commercial providers charge their customers, and is confident it can undercut these prices. The main reason, he added, is the lower cost of labor in China.
 
BGI’s website for commercial services is still under development, he said, but customers can contact the institute to find out more about services and prices.
 
BGI has provided commercial sequencing services on its Sanger sequencers since 2001, and has provided sequencing to many genome projects, including the Human Genome Project and the rice, silkworm, chicken, and pig genome projects, according to its website. Beside its next-gen fleet, the institute owns more than 100 traditional capillary sequencers, including ABI 3730xl and GE Healthcare MegaBace instruments.
 
BGI said it can currently generate 250 megabases of Sanger sequence data and 4 gigabases of next-generation sequencing data per day.
 
BGI is already offering both sequencing and bioinformatics services on its seven Illumina Genome Analyzers, which were installed in June and were initially used to sequence the genome of a Han Chinese individual (see In Sequence 9/25/2007). Meantime, the institute acquired two ABI SOLiD machines, set up about a month ago, to sequence the genome of the panda and provide service work, according to Li.
 
To help it win business in the US, the institute just recently established BGI-USA, which does not have a US office at present.
 
BGI’s next-gen sequencing services offerings include a variety of applications such as de novo sequencing, resequencing, expressing profiling, and personal genome sequencing.
 
Basic bioinformatics services are included in BGI’s sequencing service free of charge, and more advanced analyses are available for an additional charge. BGI employs more than 100 bioinformaticists, owns 10 supercomputers, has access to 2,000 CPUs, and has more than 500 terabytes in storage.
 
Advanced bioinformatics services, such as sequence assembly, gene expression analysis, or SNP discovery, are another way in which BGI hopes to distinguish itself from other service providers, although many of these also offer bioinformatics services.
 
So far, BGI has mainly provided its next-generation sequencing services to researchers in China as well as “a couple of” US-based scientists, according to Li. “Most or our foreign customers pick us because we provide a much cheaper price, and a very good service,” he claimed. A US customer did not respond to a request for comment by In Sequence.
 
Service work provides a welcome — and growing — revenue stream for the institute, Li said, which otherwise relies on government grants and income from national and international research collaborations.
 
“Providing our commercial service is probably the best way to expand our capacity,” such as hire more employees, update instrumentation and computing equipment, Li said. “We will probably double our capacity in a year.”
 
This expansion will likely include adding next-gen sequencing platforms. At the moment, BGI is evaluating both 454 Life Sciences’ GS FLX and Helicos’ HeliScope, according to Li, as the institute is “trying to catch up with the newest technologies and platforms.”
 
The reason why the first next-gen sequencing system BGI installed was Illumina’s rather than 454’s, which was also available at the time, is that Illumina contacted the institute first, Li said. “I think they were more aggressive than 454 in China,” he added, making the institute “a better offer in terms of price and customer service.”
 

“It will definitely be the most competitive price in the world.”

Some commercial providers acknowledge that BGI will increase the competition, but believe they still maintain an edge. “I do not think that BGI can offer more than we do,” Laurent Farinelli, CEO of Fasteris in Switzerland, told In Sequence by e-mail. “We have bioinformatics service for all the applications of our clients. And our costs are very competitive,” he said. Another reason for customers to go with Fasteris, which has had an Illumina Genome Analyzer since last spring (see In Sequence 4/17/2007), is its experience with the technology and its location in Europe, close to many customers. However, “as this business is worldwide, we will probably be competing,” he said.
 
Fei Lu, CEO of SeqWright, a Houston-based sequencing provider that recently acquired an ABI SOLiD sequencer, acknowledged that BGI’s prices are probably very competitive. But she pointed out that US researchers are not allowed to outsource regulatory sequencing complying with the FDA’s quality standards to a provider outside the US. SeqWright specializes in regulatory sequencing and has obtained Clinical Laboratory Improvement Amendment certification.
She also said that NIH-funded researchers cannot use their grant funding to obtain contract sequencing services from outside the US. As a result, BGI would not be able to compete with SeqWright in these two areas.
 
A major part of BGI’s experience with next-generation sequencing stems from its effort to sequence the genome of a Han Chinese individual using Illumina’s Genome Analyzer, which the institute completed in October. The researchers are getting ready to submit the results of that project to a scientific journals for publication, according to Li.
 
Based on its expertise, BGI is now also offering personal genome sequencing services to individuals, Li said. BGI is not the only provider of human genome sequencing services: GATC Biotech said in November that it is offering such services for research projects (see In Sequence 11/13/2007). Start-up company Knome told In Sequence in October that it will be offering personal genome sequence analyses to consumers (see In Sequence 10/30/2007) but has not yet disclosed who will provide its sequencing services (see In Sequence 12/4/2007).
 
The Yanhuang Project
 
But BGI is also sequencing human genomes as part of a new research project. Last week, the institute said that it signed on its first volunteer for the so-called Yanhuang Project, which was launched in April and aims to sequence at least 100 Chinese individuals in order to study genetic polymorphisms in the Chinese population.
 
According to a report from the Xinhua News Agency, the project’s name refers to “two legendary ancient emperors” believed be the founding fathers of the Han ethnic group. 
 
The anonymous volunteer — a Chinese billionaire, according to Li — donated an undisclosed amount of funding, most of which will go to the Yanhuang Project Foundation to help with future studies.  
 
According to the news report, the volunteer contributed $10 million yuan ($1.4 million) to the project. The report also said the Yanhuang Project is part of a larger comparative genomics project, a collaboration between Chinese and UK scientists, but BGI would not confirm that information.
 
Last year, BGI stated on its website that it is working with the Wellcome Trust Sanger Institute to sequence a thousand human genomes, but the institute later removed that statement. A Sanger institute researcher confirmed at the time that the two institutes are collaborating on human genome sequencing, but said it was too early to discuss specifics. He did not respond to a request by In Sequence for an update this week.
 
The Beijing Genomics Institute, founded in 1999, currently has about 1,000 employees across its three locations, in Beijing, Shenzhen, and Hanzhou. The Shenzhen branch, BGI-SZ, opened last April and is a collaboration between BGI and the Beijing Institute of Genomics of the Chinese Academy of Sciences.
 
BGI-SZ houses most of the Illumina GA’s as well as the two ABI SOLiD instruments, while the Beijing branch hosts most of the ABI 3730 Sanger instruments. The bioinformatics staff is spread about equally between the two locations, according to Li.
 
BGI-SZ is also about to break ground for a new building complex, to be completed within two years, that is funded by the local Shenzhen government, he said.

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