Private Chinese Institute Wants to Make Whole Genome Sequencing Commonplace

Pathologists and clinical laboratory managers will be surprised to learn that China is poised to become the world leader in genome sequencing! That’s due to the ambitious goals of BGI, a privately-operated institute that plans to make genomics a topic that matters for ordinary people.

“The whole institute feels this huge responsibility,” said Wang Jun, Executive Director BGI, formerly Beijing Genomics Institute, in the March 2010 issue of the journal Nature.

Now headquartered in Shenzhen, BGI is gearing up to mass-produce cheap, quality genome sequences. This, in turn, may accelerate development of cost-effective, DNA-related diagnostic tests, clinical laboratory assays, and products for patient care.

To fulfill its mission, the institute has assembled an army of young bioinformaticians. Earlier this year, BGI aquired 128 new Illumina HiSeq 2000 genome sequencers. Collectively, these powerful, new gene sequencing systems mean that BGI now has the world’s largest, next-generation sequencing capacity. About 100 of the sequencing systems were installed in BGI’s Hong Kong lab to facilitate international collaborations.

Next-generation technology is able to sequence DNA at super-fast speeds. Outputs are now thousands of times greater than older sequencing technologies. The 128 Illumina sequencing systems would theoretically allow BGI to produce 10,000 whole human genome sequences per year. This capability is more than the entire U.S. sequencing output, noted David A. Wheeler, Ph.D., Director of Molecular Biology Computational Resources at Baylor College of Medicine in Houston. “It’s clear there is a new map of the genomics world,” he said, in the Nature article.

Why China Is Now the World Leader in Genome Sequencing Capacity

“Having the largest DNA sequencing facility in the world in Hong Kong will hopefully contribute towards attracting talent in genomics and bioinformatics and stimulate collaboration with other local research groups, such as those in the two medical schools,” said Dr. Dennis Lo, Director of the Chinese University of Hong Kong’s (CUHK) Li Ka Shing Institute of Health Sciences, in the Nature Biology article.

“BGI’s investment in Illumina’s new HiSeq 2000 system is an important step in our effort to develop a premier sequencing facility that serves scientists globally,” declared BGI’s Vice President, Xiuqing Zhang, in a recent issue of Nature Biology. “Our goal is to build partnerships and collaborations around the world that contribute to our global society. Creating solutions that enhance agriculture and food production, for example, are a key focus for us, [as are] more region-specific programs, such as the development of the personal genomics field in China.”

Now equipped with the world’s greatest capacity to sequence genomes, BGI has the challenge to pay for all its new sequencing systems, which carry a retail list price of 3.4 million Yuan Renminbi each, or (US) $690,000. BGI’s strategy is to grow international collaborations fast enough to pay for all that new equipment. Currently it employees 1,500 people. It expects to add 2,000 employees in 2010 as is sequencing production line ramps up.

BGI’s founder is Yang Huanming, Ph.D., also known as Dr. Harry Yang. He doesn’t apologize for reducing science to an assembly line. In fact, he suggested in the Nature article that BGI brings little intellectual capital to projects. “We are the muscle, we have no brain,” he announced.”

However, Yang’s comment belies a core belief by the BGI team—from the top down to the newest recruits—that the institute’s work can have a significant impact on such fields as medicine, biology, and agriculture.

Despite the lack of Ph.D.-trained scientists, BGI has established itself as an important genome center. It successfully sequenced 1% of the human genome for the International Human Genome Project and contributed 10% of the International Human HapMap Project, along with CUHK.

Among BGI’s more impressive achievements, as published in top tier journals, are the genomes of rice, cucumber, silkworm, Great Panda, and an ancient human. In 2003, BGI sequenced the corona virus that caused severe acute respiratory syndrome (SARS) and developed a useful diagnostic kit.

More recently, the institute launched the first of thousands of proposed projects aimed at creating a genomic tree of life. This will include 10,000 microbial genomes, along with the genomes of 1,000 species of plants and animals. The work is moving forward and following the completion of sequencing, the genomes of the first 1,000 species of gut bacteria were published in the same issue of Nature. The data was a showcase of BGI’s sequencing power, which required it to compile 577 billion base pairs of sequence data.

Experts believe BGI’s example may also stimulate similar infrastructure development elsewhere. Richard Wilson, Director of The Genome Center at Washington University School of Medicine in St. Louis told Nature Biology that “If countries such as the United States, the United Kingdom, or anyone else sees that as a good reason to build up their own genetic sequencing infrastructure, I think that’s a good thing. The more the better.”

–P. Kirk

 

Related Information:

Chinese bioscience: The sequence factory

Chinese institute makes bold sequencing play

A human gut microbial gene catalogue established by metagenomic sequencing