The Gene GeniesGene Sequencing Brings a Breakthrough

On May 8 this year, the "Rong-Yang Team"-a joint venture by researchers from Veterans General Hospital and National Yang Ming University-announced its completion of the initial sequencing of 10 million bases of the human genome, part of a two-year project.

The team's achievement was greeted with acclaim and received in-depth coverage in the press, stimulating public curiosity about the work of gene sequencing.

The mapping of genomes has profound significance for the science of life. According to Chiang Hoang-yung, manager of the Development Center for Biotechnology, the genome projects of the 1990s are regarded as equivalent in importance to the Manhattan Project of the 1940s-which resulted in the creation of the A-bomb-and the Apollo program of the 1960s-which put the first man on the moon.

Wu Cheng-wen, president of the National Health Research Institute, describes genetic technology as "the biggest revolution in history," saying: "The birth of molecular biology and genetic engineering in the past 40 years has changed the face of the science of life."

The human genome and rice genome projects have both been the focus of intense international interest.

The Human Genome Project was launched in 1990 by the National Institutes of Health in the US and the Wellcome Trust in the UK. It involves eighteen countries, headed by the US, the UK, Japan, Germany, France and mainland China. The project was originally scheduled for completion in 2005, but intense competition from a privately owned gene-sequencing company, Celera Genomics, spurred the multinational team to bring forward its timetable, and a full, precise map of the human genome is now expected before 2003. Early last year Taiwan's Rong-Yang Team joined the project, taking on the sequencing of one part of chromosome 4.

It is also anticipated that the genetic code for rice will have been fully deciphered by 2003, through the Rice Genome Sequencing Project (IRGSP), the world's largest program for gene sequencing of a food crop. This, it is hoped, will prove useful in the effort to solve the increasingly pressing problem of food shortages in the coming decades.

The rice genome project unites teams from Japan, the UK, France, the US, Singapore, mainland China, Thailand, Canada, India, South Korea and Taiwan. Academia Sinica's Institute of Botany has been involved since February 1999, and is working on sequencing rice chromosome 5.

Shaw Jei-fu, director of Academia Sinica's Institute of Botany, says: "This work will become an indelible part of history." Participation in the international rice genome project helps boost the institute's academic standing, and opens the door for improved exchange of technology and data.

The Rong-Yang Team, however, has been less fortunate in terms of benefiting from international cooperation. Just as Taiwan is shut out of the United Nations, the Rong-Yang Team has not received due international recognition for its work on the Human Genome Project. But as team member Hsiao Kwang-jen notes: "Our efforts prove that we have the necessary capability. We have done everything required of us, and that's that."

What exactly are genes?

Chromosomes, which carry the genetic blueprint for living organisms, are formed of tightly coiled strands of DNA, in which four chemical bases-designated A, T, G and C-are paired together in different combinations along a double-helix-shaped molecular chain. Certain sequences of base-pairs along these DNA strands form genes, and the totality of base pairs makes up the "genome." Sequencing the bases from which genes are formed is the first step towards mapping the genome and unraveling the genetic code of any particular organism.

Human beings have 23 pairs of chromosomes, comprising 3 billion such base pairs. Chromosome 4, which was selected for research by the Rong-Yang Team, has around 200 million base pairs, of which the team concentrated on sequencing a segment (designated q22-q24) of around 10 million bases.

Chou Chen-kung, professor at Yang Ming University's Institute of Genetics, explains that chromosome 4 was selected because of research by National Taiwan University professor of internal medicine Chen Pei-she, who found that chromosome-4 genetic defects and aberrations were particularly common among victims of liver cancer-Taiwan's leading cause of death by cancer.

Rice has 12 chromosomes comprising 430 million base pairs, about one-eighth as many as in the human genome. According to Wu Hong-pan, a researcher at Academia Sinica's Institute of Botany, the Academia Sinica team opted to sequence rice chromosome 5 because its genetic markers are relatively distinctive, and it is not too long. Furthermore, this is the chromosome containing genes related to disease resistance, photosynthesis, carbohydrate metabolism, and storing proteins and enzymes, which raises the prospect of finding the genetic cause for one of Taiwan's major forms of rice blight.

A distinctive feature of gene sequencing projects is the need for collaboration among specialists with different areas of expertise. The Rong-Yang Team, and the Academia Sinica group working on the rice genome, are good examples of this cooperative model.

"The days when a project depended on one person are gone," says Chen Ching-san, researcher at Academia Sinica's Institute of Botany.

The team for the rice genome project includes: Chen Ching-san, who has long experience in rice research and special expertise in the fields of genetic engineering, molecular biology and biochemical analysis; Chou Teh-yuan and Hsing Yue-ie, also experienced in rice research and particularly strong in sequencing analysis; Wu Hong-pan, an expert on rice genetics and computer analysis; and institute director Shaw Jie-fu, who is distinguished for his work on plant gene functions.

The Rong-Yang Team's human genome sequencing work is being carried out across three laboratories, headed by Veterans General Hospital Department of Medical Research members Chou Chen-kung and Chang Tai-chieh, along with Yang Ming University professors Hsiao Kwang-jen, Tsai Shih-feng and Yang Ueng-cheng.

Gene sequencing is an involved, repetitious process requiring extreme precision. Tsai Shih-feng, who is in charge of the sequencing work, says that the Rong-Yang Team repeats each step in the process ten times for each base, to minimize the number of intervals in the data. Tsai says that the Rong-Yang Team has achieved a level of continuity five times higher than for the equivalent sequencing work in the US. For every 100 bases sequenced in the US, there are 10-20 breaks in the data, compared with a figure of 3-5 achieved by the Rong-Yang Team.

Once the laboratory has established a sequence of bases, the data is submitted for computer analysis and assembled according to its position in the chromosome.

Yang Ueng-cheng, who oversees genetic analysis for the Rong-Yang Team, explains that a huge volume of repetitive data is produced by the work. "The useful information is hidden among a lot of extraneous material. How best to manage and analyze these vast quantities of information, in order to accelerate the pace of bio-medical research, is an important question for the post-genome age."

The Rong-Yang Team located over 200 genes among the 10 million bases it was working on. According to Yang Ueng-cheng's analysis, 30 of those are known genes (for which information is held on existing databases) 156 are "predicted" genes (for which there is only incomplete data at present) and 36 are unknown genes (for which no previous data exists). This last category of genes is the one that gets the researchers excited. The main follow-up work involves verifying the existence of the newly found genes, and understanding their functions.

Chang Tai-chieh, associate professor in bio-medical technology at Yang Ming University, works on authenticating the results of computer analysis. He says that of the unknown genes, two have been found to have special features, one of them being found in the cancerous tissue of seven out of ten cases of lung, breast and stomach cancer. This is a major discovery that will become the focus of further research. "Bio-medical disease research is the priority for future work," says Chang.

"Genetic research is the most important form of research for the 21st century," says Chou Chen-kung. By integrating the full range of research activities, the Rong-Yang Team has now established a method and structure for subsequent research. "From now on, so long as the funding is there, we can research any kind of gene."

The Rong-Yang Team has considerable strength in terms of its gene sequencing capability. Hsiao Kwang-jen, professor of genetics at Yang Ming University, points out that the team is one of only 20 or 30 units in the world capable of sequencing 10 million bases in a year. As Tsai Shih-feng says, the Rong-Yang Team provided 0.3% of the total data for the Human Genome Project, putting it on a par with the contributions from Germany, France and mainland China, and ranking Taiwan seventh in the world in terms of its gene sequencing capability.

But how important is it to have the capability to do gene sequencing?

Genetic research is based on information accumulated in gene databases. In recent years, research techniques have progressed from the single-gene method to the multiple-gene approach of genomics. Tsai Shih-feng explains while single-gene research is still valid, there is the risk of "not being able to see the forest for the trees." The relations among genes only become apparent once various genes are sequenced together.

Wu Cheng-wen, president of the National Health Research Institute, says that one reason Taiwan can't afford not to be involved in work on the human genome, is the fact of the biological distinctions that exist among different races. "We need to establish a genetic database of our homeland if we are to better research the diseases that are unusually prevalent here, such as liver cancer and nasopharyngeal cancer."

The data that results from human gene sequencing has to be registered internationally and posted on the Internet, so it can be used as a public resource. But this only applies to the sequence in which the bases are arranged. Subsequent discoveries concerning newly located genes and their connection with particular diseases become the intellectual property of the relevant researchers, who can apply to patent those discoveries. The mapping of the human genome, therefore, marks the beginning of a new round of competition-to discover the functions of newly found genes.

Hsiao Kwang-jen compares gene sequencing to taking a satellite photo of the Earth. The genetic map serves as a tool, but the objective for scientists is to decipher the information contained therein, and pinpoint the connection between particular genes and particular diseases. This is why genetic research raises the prospect of enormous commercial opportunities.

The unraveling of the enigma of the human genome brings with it the hope of treatment for hitherto incurable hereditary diseases, immunodeficiency diseases and cancer.

Diseases traceable to a single gene defect are a special focus of research. It is estimated that 5000 kinds of disease in people are caused by single gene defects, including Huntington's disease, thalassemia, and "brittle bone disease." It is hoped that gene therapy can take the place of bone-marrow transplants and other forms of treatment used at present, massively boosting the cure rate for many diseases.

High hopes have been pinned on gene therapy in recent years, in the belief that it represents a lifeline for people suffering from otherwise incurable conditions. However, last December an 18-year-old American died during gene therapy testing, triggering controversy about the approach and virtually shutting down some research programs. Fortunately, in April this year researchers in France announced that they had successfully used gene therapy to treat three baby boys suffering from hereditary immunodeficiency conditions. This was the first major breakthrough in the last ten years, during which gene therapy has been applied in more than 4000 cases around the world, and it reignited hope in the prospects for the technique.

In the same way, the decoding of the rice genome has spurred developments in a number of related areas.

Shaw Jei-fu explains that food shortages will be an increasingly important problem in the future, and rice, which is Asia's leading food crop and is second only to wheat in terms of global output, has obvious importance. Decoding the genetic make-up of rice creates a foundation for subsequent research into the prevention of rice diseases, improved quality, and increased yields.

The mapping of the rice genome also helps researchers to enhance their knowledge of other food crops.

Hsing Yu-yi, a researcher at Academia Sinica's Institute of Botany, explains that among food crops, rice has the smallest genome. The wheat genome, for example, is larger by a factor of 37-larger even than the human genome. Most plants in the grass family-of which rice is a member-share a similar genetic profile, which means that information about the rice genome can also be applied to crops such as sorghum, maize and sugarcane.

It is worth noting that despite the remarkable accomplishments of the Rong-Yang Team and the rice genome group at Academia Sinica, there is concern that Taiwan may already be losing out in race for genetic technology.

"Taiwan is rapidly losing the hard-won position of strength that has been built up over the past eight years," says Tsai Shih-feng. Taiwan began preparing for involvement in gene sequencing work over two years ago, but during the past 18 months the pace of research elsewhere in the world has accelerated, with shorter timetables and increased investment. But there was no adjustment in the pace of research in Taiwan. "It's like a mine filled with innumerable treasures. While others have introduced new types of equipment, we're still chipping away with the same old tools," says Tsai Shih-feng, describing the conditions for biotechnology research in Taiwan at present.

A workman has to sharpen his tools if he is to do a good job. One measure of comparison is the level of investment in gene-sequencing equipment. Tsai Shih-feng has written that more than 1000 new capillary electrophoresis sequencing machines have been installed around the world during the past year, but only one of those was in Taiwan. Mainland China became engaged in the gene sequencing project just one year ago, but already has 40 of the new machines, and this number is expected to rise to 100 in the near future.

Published research findings are another measure of comparison.

Chou Cheng-kung says that a total of over 2000 papers are published every year in Nature, and Science, the scientific community's two most authoritative periodicals. But there have only been a couple of contributions from Taiwan during the past five years, neither of which concerned bio-medicine. "We are far behind in terms of total output," says Chou. Less molecular biology research is happening in Taiwan than at any single top university in the US. "We're only fooling ourselves if we don't face up to the fact that we are lagging behind."

What kind of role can Taiwan play in the field of biotechnology? This is a fundamental issue, one which the relevant organizations will have to address. "If we don't get a boost, then pretty soon we'll be out of contention," warns Chou. "Government and academia must realize that the only solution is to recognize that we're dropping behind, and come up with a plan for catching up."

Academia Sinica president Lee Yuan-tseh, addressing the Fourth Strategy Conference for the Biotechnology Industry, described two main strategies for promoting scientific research. One is "putting the cows out to graze"-providing funding that enables scientists to freely carry out research. The other is to establish a huge team, and go all out in one particular area of research. At present, the National Science Council's approach is to provide researchers with funding-putting the cows out to graze. But the pasture is too small and there's not enough grass to go around, so none of the cows can eat their fill.

Shaw Jei-fu points out that in other countries, industry is extremely enthusiastic about investing in research projects, whereas Taiwanese industry is more conservative in this regard. Relying on limited government funding, however, makes it very hard for scientists to achieve a breakthrough. There has recently been some good news in this respect, however, with Lee Yuan-tseh raising some NT$3 billion from industry for the Academia Sinica to use for developing cutting-edge technologies, including technology connected with functional genomics research.

"Onwards and upwards, or we sink into the mire," says Tsai Shih-feng, quoting a slogan that has been bandied about in Taiwan ever since the presidential election. Genetic research in Taiwan is at a make-or-break point in its development. It was presumably with mixed feelings that members of Taiwan's Rong-Yang Team observed the global acclaim that greeted the recent completion of the preliminary draft of the human genome.