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Monday, July 12, 2010

BGI: Beijing Genomics Institute

In an earlier post I mentioned BGI (formerly Beijing Genomics Institute, now located in Shenzhen). Below are some excerpts from a Nature article about the Institute, which is funded by a $1.5 billion dollar (!) loan from the China Development Bank.

Some of the researchers at BGI are very young -- the article profiles two who are in their early 20s and already have significant responsibility. Is this really so strange? After all, people who lead teams at startups or at Google or FaceBook, developing key infrastructure, are often not much older.

Nature even ran an editorial about this: Do scientists really need a PhD? Bioinformatics is a good field to try this in as it is computing intensive (even youngsters can produce good code) and a relatively new field (the background genetics and statistics can be taught fairly quickly to smart kids). On the opposite end of the spectrum: particle or string theory, in which even supersmart kids will barely have their footing after 3-5 years of post-BA work. The contrast between fields in which people can quickly get started in research, versus those that have a steep learning curve and lots of accumulated depth, makes for constant misunderstandings and debates over how graduate education should be structured.

Below are pictures of BGI's director and two of the young researchers.

Nature: In 2006, Li Yingrui left Peking University for the BGI, China's premier genome-sequencing institute. Now, freckled and fresh-faced at 23 years old, he baulks at the way a senior BGI colleague characterized his college career — saying Li was wasting time playing video games and sleeping during class. "I didn't sleep in lectures," Li says. "I just didn't go."

He runs a team of 130 bioinformaticians, most no older than himself. His love of games has served him well when deciphering the flood of data spilling out of the BGI's sequencers every day. But "science is more satisfying" than video games, he says. "There's more passion."

The people at the BGI — which stopped officially using the name Beijing Genomics Institute in 2007 after moving its headquarters to Shenzhen — brim with passion, and an ambition so naked that it unsettles some. In the past few years the institute has leapt to the forefront of genome sequencing with a bevy of papers in top-tier journals. Some recent achievements include the genomes of the cucumber1, the giant panda2, the first complete sequence of an ancient human3 and, in this issue of Nature4, the genomes of more than 1,000 species of gut bacteria, compiled from 577 billion base pairs of sequence data.

The mission, BGI staff say with an almost rehearsed uniformity, is to prove that genomics matters to ordinary people. "The whole institute feels this huge responsibility," says Wang Jun, executive director of the BGI and a professor at the University of Copenhagen. The strategy is to sequence — well, pretty much anything that the BGI or its expanding list of collaborators wants to sequence (see 'Mass production'). It has launched projects to tackle 10,000 microbial genomes and those of 1,000 plants and animals as part of an effort to create a genomic tree of life covering the major evolutionary branches. Important species, such as rice, will be sequenced 100 times over, and for humans there seems no limit to the number the institute would like sequenced.

To fulfil that mission, the BGI is transforming itself into a genomics factory, producing cheap, high-quality sequence with an army of young bioinformaticians and a growing arsenal of expensive equipment. In January, the BGI announced the purchase of 128 of the world's newest, fastest sequencers, the HiSeq 2000 from Illumina, each of which can produce 25 billion base pairs of sequence in a day. When all are running at full tilt, the BGI could theoretically sequence more than 10,000 human genomes in a year. This puts it on track to surpass the entire sequencing output of the United States, says David Wheeler, director of the Molecular Biology Computational Resource at Baylor College of Medicine in Houston, Texas. "It is clear there is a new map of the genomics world," he says.

The charge that the BGI has reduced science to brute mechanization does little to ruffle feathers in Shenzhen. Wang himself quips that the BGI brings little intellectual capital into projects: "We are the muscle, we have no brain." But such comments belie a quiet confidence, in everyone from the BGI's seasoned management to its youngest recruits, that they can make an impact not just to the balance of sequencing power but also in biology, medicine and agriculture. This will be a challenge given the significant loans taken out to expand capacity. Torn between scientific and financial goals, even its founder can't seem to decide whether the BGI is a business or a non-profit research institute. Genome scientists around the world are watching to see how it will strike a balance.

... With this breathing room, the BGI has grown to employ 1,500 people nationwide, more than two-thirds of them in Shenzhen, and this is expected to jump to 3,500 by the end of the year. With the investment in new sequencers, provided by a 10-billion-renminbi loan from the China Development Bank, the BGI's capacity will grow, but so will costs.

... The BGI's Luo Ruibang, also a student at the South China University of Technology in Guangzhou, turned 21 while at his last scientific meeting. He says he's had trouble convincing other scientists that, lacking doctoral training, he can do top-notch science. "A lot of the foreigners wonder if I'm really capable," he says. Luo and Li were co-first authors on a paper9 describing the discovery of large DNA segments in the Asian and African genomes that are absent in the Caucasian genome.

Li and his bosses are confident that this youth brigade can piece together and verify sequences. "It is a new field," says Wang. "There is not much experience anyway." But interpreting data and designing experiments are two different things, and BGI staff admit a dearth of knowledge in the latter. "We don't know much about biology," Li says. Liu says the BGI needs to overcome its biological blindspot, but he is supportive of its mission. "They are primarily sequencers, but smart ones with big guns," he says.

... Research alone is not going to pay back the 10-billion renminbi bank loan. The BGI makes some income from collaborations, which account for 40% of the sequencing workload. Outsourced sequencing services for universities, breeding companies or pharmaceutical companies bring in higher margins and account for another 55% of the workload (the final 5% is the BGI's own projects). In 2009, the BGI pulled in 300 million renminbi in revenue. That is not enough, says BGI marketing director Hongsheng Liang. In 2010, Liang hopes to pull in 1.2 billion renminbi.

New income could come from proprietary rights to agricultural applications. The BGI, which owns more than 200 patents, has been attempting to do genomics-based breeding with foxtail millet in Hebei and has other agricultural projects in Laos. More cash could come from expansion of services overseas. Within three years, the institute plans to open offices in Copenhagen and San Francisco. The BGI may also charge for access to its Yanhuang database, a project launched in 2008 to sequence the genomes of 100 Chinese; BGI scientists say they would like to expand this number into the thousands. Although according to Yang, it would be charging "at cost" — to cover computational expenses and maintenance, not for the data. ...

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