HK to become world genomics research hub

PUBLISHED : Monday, 27 December, 2010, 12:00am
UPDATED : Monday, 27 December, 2010, 12:00am

Hong Kong is poised to become an international gene sequencing and genomics research hub, thanks to Beijing's drive to turn the country into an international science powerhouse by 2020.

Already it is housing some of the world's most powerful supercomputers and gene sequencers, the result of the mainland's dominant genomic company, BGI, using the city to host its key laboratory.

Working at the blinding speed of supercomputers, BGI Hong Kong will theoretically be able to sequence 1,300 human genomes every day. By comparison, the Human Genome Project took more than 10 years to unravel the human genome.

'To put that in perspective, [BGI] has about the same capacity as the three largest genome centres in the United States, including the Broad Institute, Washington University and Baylor College of Medicine combined,' said Kevin Davies, editor-in-chief of the American magazine Bio-IT World. BGI was also much larger than Asia's other DNA sequencing centres, Davies said, referring to Macrogen in South Korea and NIG and Kazusa in Japan.

Gene sequencing is a research tool and the basis of biotechnology. For example, in medicine, it helps to identify genetic abnormalities and hereditary diseases, and to produce new drugs. In agriculture, the genes of crops are modified to enhance desirable features and eliminate undesirable ones. In biology, researchers study the evolution of organisms by pinpointing their genetic mutations, or changes in the genetic sequences that were passed on to the next generation by natural selection.

An old printing factory on Tai Po Industrial Estate now houses BGI Hong Kong's four-storey laboratory, which is engaged in an unparalleled DNA sequencing project that may grab global attention; earlier discoveries from its parent institute, BGI, have already been published in some of the world's leading scientific journals, such as Nature and Science.

Inside, Alex Wong Lap-chi, executive director of BGI Hong Kong, presides over the laboratory's 58 Illumina next-generation sequencers. Each costs about 3.4 million yuan (HK$4 million). Another 57 HiSeq 2000 advanced gene sequencers would be shipped from the US by the end of January, he said.

When all those genome analysers are running around the clock, electricity for the computer and cooling systems alone will cost 9 million yuan a year. The analysers will be supported by another 22 on the mainland, backed by 1,500 bioinformatics specialists working mainly in Shenzhen.

The world has already seen some of BGI's capabilities. In March, the cover pages of Nature reported on its sequencing of an ancient human genome, 4,000-year-old extinct Palaeo-Eskimo remains from Greenland. Last year, Nature featured BGI's draft sequencing of the genome of three-year-old female panda Jing Jing, one of the Beijing Olympics mascots.

At present, BGI is aiming to sequence the genomes of 1,000 plants and animals and 10,000 microbes to expand its own database of genomic information. It has launched an ambitious but controversial project to hunt for the genes responsible for human intelligence.

It is also undertaking sequencing projects for profit to pay back a 10 billion yuan bank loan. The institute has already scored one important client - the pharmaceutical company Merck, which announced a five-year deal with BGI two months ago. Other drug firms such as GlaxoSmithKline, Pfizer, Lilly and Novartis have also shown interest in the Hong Kong facility.

Genomics is among the physical sciences that Beijing wants to champion as an industrial policy goal, and BGI is at the forefront of genomic science on the mainland.

BGI started life as the Beijing Genomics Institute. The central government set it up in Beijing in 1999 when it decided to join the international Human Genome Project and sequenced 1 per cent of the total human genome. BGI relocated its headquarters to Shenzhen in 2007.

In April this year, the institute set up its Hong Kong sequencing centre, financed with part of a 10 billion yuan low-interest loan from the state-run China Development Bank. The Hong Kong centre is to handle most of the institute's international genomics business, taking advantage of the city's scientific research capability and easier customs facilities for importing biological specimens such as blood, tissue and urine.

BGI now has a staff of 3,000 at six research centres across the mainland, Hong Kong and centres in Boston and Copenhagen. About 100 bioinformatics specialists work at the Hong Kong facility and about 1,500 at BGI's Shenzhen headquarters to analyse and interpret the reams of DNA data churned out by the sequencers.

Those 1,600 specialists are a huge asset, says Sumio Sugano, bioscience professor at the University of Tokyo. 'They are all under 30 and these young brains with world-top capability of sequencing and computing power could make BGI the future Apple, Microsoft or Google in the genomics field,' Sugano said, and the influence could reach beyond medicine to agriculture and green energy.

No single institute in the US or Europe can afford 1,600 bioinformatics specialists, but the mainland's cheaper labour market makes it possible. Labour is usually about one-third of the cost of sequencing (reagents, computing and capital expenditure make up the rest).

BGI is hiring Chinese specialists in computer science, biology, mathematics, statistics and genetics at about one-fifth the price its US and European counterparts must pay.

BGI technology director Li Jingxiang said it was difficult to recruit bioinformatics specialists in Hong Kong because many fresh graduates with related backgrounds joined the financial sector. And because technicians in Hong Kong cost more than BGI is used to paying, the number of such specialists will be kept to a minimum in Tai Po, with most IT work done in Shenzhen.

Not everyone is impressed with BGI. Pseudo-science debunker Dr Fang Shimin , better known as Fang Zhouzi , said large-scale sequencing resembled a labour-intensive Henry Ford assembly line. While acknowledging that information generated from DNA sequencing is very useful for geneticists and biologists, he said sequencing simply was not an innovative activity.

'Basically, genome analysers will sequence automatically as long as you can afford these expensive machines,' the Beijing-based biological chemist said. 'BGI's work is more like a transcriber that simply copies down crude DNA data from organisms, but that doesn't mean BGI understands what it is writing about.'

But biology professor Samuel Sun Sai-ming from the Chinese University of Hong Kong said he was confident BGI could make major contributions. It would not mean much to genomic science if BGI simply sequenced DNA alone, Sun said. 'But BGI has thousands of bioinformatics specialists to manage, analyse and interpret the huge amount of DNA sequence data, making biological sense of the DNA sequences. It can mine the data and make discoveries in biological and medical sciences and for further applications.'

Kelvin Lee, a professor of chemical engineering at the University of Delaware, said that because life-sciences research relied heavily on access to large amounts of high-quality sequencing data, BGI was capable of providing the foundation of knowledge needed for the study of genomics to move forward this century.

Last year, BGI launched a 400,000 hectare project with the government of Laos, exploring the possibility of turning genetically modified plants such as cassava, sugar cane, oil palm and castor oil into food, biological alcohol or diesel oil within five years.

Yin Ye , a BGI vice-president, said the institute's ambitions included cutting the cost of sequencing a human genome from less than US$10,000 this year to US$2,000 - and eventually to an affordable level for everyone. The Human Genome Project, which published its first rough sequence of mankind's genetic code in 2001, cost an estimated US$3 billion.

Jay Flatley, chief executive of the world's leading genome sequencing company, Illumina, based in California, predicts DNA sequencing will become so cheap that babies born from 2019 onwards will have their genetic code routinely mapped at birth.

Dennis Lo Yuk-ming, a professor of medicine at Chinese University, hopes the presence of such a large facility will raise Hong Kong's profile in the global genomics community.

'BGI's achievements show that with timely funding, Asian scientists can compete at the highest level on the world stage,' he said.