Genomics for North-South collaboration

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Genomics for North-South collaboration
Claire Fraser

This autumn, the complete genome of one of the worst scourges of the developing world — the parasite Plasmodium falciparum, which causes malaria — will be published after six years of effort by an international team of researchers.

Shortly afterwards, a smaller but equally dedicated group of scientists will finish sequencing the genome of Theileria parva. This parasite causes East Coast fever, which kills more than one million cattle a year in sub-Saharan Africa.

Both of those landmark projects, in which The Institute for Genomic Research (TIGR) — a not-for-profit research institute based in Maryland — has played a central role, have the long-term potential to help millions of people in the developing world. And the second also offers a model of how scientists can help bridge the North-South gap in genomic research by cooperating on projects of mutual interest.

Through projects such as these, I believe the genomics revolution can do its part to help countries both in Africa and elsewhere achieve sustainable development over the long term.

Earlier this year, a report * by the World Health Organisation (WHO) emphasised the need to focus on genomics — as well as its applications in medicine and related fields — on diseases that are common in developing countries. This report makes clear that the potential applications of genomics are tremendous, helping researchers develop not only vaccines and medications, but also more efficient diagnostic techniques.

Because genomics has transformed much of biology into information science, any researcher with access to the Internet and some training in bioinformatics now has the potential to make significant discoveries using public databases.

In theory, therefore, the globalisation of DNA and protein databases could lead to greater scientific collaboration worldwide. But, as the WHO genomics report points out, wide disparities in resources means that that the playing field for researchers in developed and developing countries is not level. Sequencing machines are costly, as are computers to analyse and store the sequencing data.

For those reasons, it is important for research institutes in industrialised nations to form partnerships with counterparts in developing countries to work toward common goals. An example of such a productive collaboration is the one that links TIGR with the International Livestock Research Institute (ILRI) in Nairobi, Kenya.

TIGR employs a number of researchers from Africa, Asia and Latin America. Its mission is to use genomics to explore the diversity and complexity of life, and explore the application of basic research in medicine, agriculture and other fields. This mission intersects with the goals of ILRI in our joint project to sequence and annotate the genome of Theileria parva, which affects thousands of families whose livelihoods depend on their cattle.

The T. parva genome has now been fully sequenced and is in the process of being annotated. We are looking forward to the next steps that will involve transforming that genomic data into useful tools within an African context.

For example, certain similarities between the Plasmodium and Theileria parasites — both of which are transmitted by bloodsucking arthropods and later invade host blood cells — means that a comparison of the two genomes may give us insights into candidates for vaccines against both parasites.

East African Cow

Moreover, T. parva kills cattle by causing infected white blood cells to multiply and invade host tissues, much in the way that cancer cells do. However, we don’t yet fully understand how the parasite does this. Sequencing of the T. parva genome might deepen our understanding of cancer biology by helping to pinpoint the genes that initiate the unrestrained cell division that causes tumors.

There are already several other successful examples of international cooperation in genomic research. For example, later this year the International Rice Genome Sequencing Project will complete — and place entirely in the public domain — a high-quality draft sequence of the japonica sub-species of rice.

Japanese labs are leading this group, which also includes scientists in the United States, India, Korea, Brazil, Taiwan, France and China. With the japonica genomic information, researchers may be able to develop new varieties of rice that have a greater nutritional value and are also less susceptible to drought, improvements that could help millions of people in the developing world.

One way in which genomics is opening new doors to scientists around the world is through secure, rapid access to the Internet that allows them to download data at no cost from Genbank in the United States and other sources of genomics information.

Furthermore, the expansion of bioinformatics and biotechnology training means that scientists in developing countries have the potential to create their own diagnostic tools and efficient, economical vaccines, giving such countries greater leverage in negotiations with potential collaborators in the developed world.

Some developing countries are already taking on their own sequencing projects. One of the best examples has been Brazil’s search for new ways to control the Xylella fastidiosa bacterium that causes a devastating disease of orange trees. To tackle the problem, Brazil created a consortium called the Organisation for Nucleotide Sequencing and Analysis (ONSA) that coordinated the work of 30 Brazilian laboratories to sequence the Xylella genome.

More recently, Brazilian researchers have made another significant advance by sequencing two major plant pathogens of the genus Xanthomonas. In a paper published earlier this year in Nature (see related articles below), the Brazilians compared the genome of a Xanthomonas bacterium that causes citrus canker with a related species that causes “black rot” in broccoli and cabbages.

These results demonstrate that developing countries can already hold their own in the big league of genomics. For example, Brazil’s sequencing efforts means that it has inserted itself into the international genomics loop as a player that can both offer invaluable information to the world’s research community and set its own priorities.

Claire Fraser

It is clear that genomics has the potential to help alter the paradigm of North-South relations. As scientists in developing countries increase their ability to acquire and use the fruits of the genomics revolution, they will become more important players in the scientific world. Furthermore, diseases such as East Coast fever, once considered to be strictly regional, will find their place on the world’s scientific stage.

Such trends indicate that the paradigm of the relations between North and South is already shifting in a way that is allowing the web of international interdependency in scientific research to transcend the hurdles of geographical separation.

Claire M. Fraser is president and director of The Institute for Genomic Research (TIGR), Rockville, Maryland, USA.

Photo credits: ILRI