Research Article: Molecular Genomic Approaches to Infectious Diseases in Resource-Limited Settings

Date Published: October 26, 2009

Publisher: Public Library of Science

Author(s): Josefina Coloma, Eva Harris

Abstract: Josefina Coloma and Eva Harris discuss advances in genomics in resource-limited settings and argue that access to training and capacity building in bioinformatics and data mining will be crucial for the future

Partial Text: Only half a century after the landmark discovery of the double helix structure of DNA, the human genome was sequenced and a new era of biomedical research was ushered in [1]. Parallel advances in comparative genomics, genetics, high-throughput biochemical techniques, and bioinformatics have provided researchers in wealthy nations with a repertoire of tools to analyze the sequence and functions of organisms at an unprecedented pace and level of detail. Since the beginning of the genomics era [2],[3], however, it has been evident that researchers in many developing countries will not be participating fully in genomics research, mainly because of their technological isolation and their limited resources and capacity for genomics research combined with the urgency of many other health priorities. To share the benefits of this technology equitably worldwide, some have advocated that developed and developing countries alike should participate in genomics research to prevent widening of the already large gap in global health resources [4]. As most of the funding that has fueled the rapid advance of the field comes from developed country governments, private initiatives, and industry, however, not much has been done to enable poorer countries to participate as equals in genomics research. Developing countries that are not directly participating in a genomics initiative can, nonetheless, gain from the discoveries of this field in a number of ways, as detailed below. It remains to be seen, however, how the developing world will specifically benefit from the refined genetic information and the drugs and vaccines produced as a result of genomics initiatives. Information exchange and translation of knowledge must be carried out continually through fora accessible to researchers in developing countries. “North–South” collaborations—starting with capacity building in genomics research—need to be fostered so that countries that are currently excluded from the genomics revolution find an entry point for participation. “South–South” collaborations must be encouraged to allow countries with limited resources to pool their human and financial capital, learn from each other’s experience, and share in the benefits of genomics. Ensuring that the benefits of genomics-based medicine are shared by developing countries involves their inclusion in the discussion of ethical, legal, social, economic, and sovereignty issues (Box 1).

In the developing world, the link between human genomics and infectious disease is particularly important. The influence of host genes on the differential susceptibility of individuals or populations to infection and the evolutionary influence of pathogens on the genetic composition of populations by selecting for resistant individuals through coevolution can be now dissected in more detail with genomics. An array of host–pathogen interactions are associated with particular human genes and loci, as best illustrated by the relationship of the malaria pathogen with host genetic evolution. As genetic information about larger populations becomes increasingly available, it is important to disseminate information relating genomics to disease as well as to devise intervention strategies for at-risk populations worldwide [5].

Although the genomics initiatives described above challenge the notion that developing countries must wait to import advances in science and technology that emerge from the developed world, poorer developing countries still do not have the resources to develop their own genomic projects on a large scale. However, implementing simpler molecular genetic approaches to solve health problems is very feasible in resource-limited settings. The decades preceding the human and microbial genome initiatives were highlighted by important developments in molecular and genetic methods applied to infectious diseases. These developments were enabled by increasingly available genetic information about many pathogens and their vectors and by molecular tools such as PCR and powerful sequencing technologies, which permitted rapid advances that were successfully introduced into the developing world with little delay.

General international ethical and scientific guidelines for genomics have been created and are being adapted by nations participating in the field as it evolves. Governments and regulatory agencies in the “North” have prepared for the eventual implementation of genomics-based medicine in their respective countries. A critical problem faced by developing countries is the lack of national guidelines for genomics research and its ethical ramifications. Thus, a priority to be set by countries in the early steps of genomic applications is to draw up the necessary rules and legislation on genomics and to generate procedures for implementation. Creating the necessary communication channels between researchers, social scientists, policy makers, and civil society organizations is also a critical step. Other key challenges facing emerging genomics researchers include proper informed consent and privacy protocols for research participants, protecting them against the potential discrimination that might emerge from genetic information and ensuring that any benefit that comes to fruition from the research reaches them. In parallel, capacity building of scientists in clinical research and of ethics committees in these issues is essential. Past experience with “safari research” in which biological samples are taken out-of-country for research that does not benefit local populations have prompted countries such as Mexico, India, and Brazil to draw up legislation governing “sovereignty” over genomics material and data that restricts the export of biological materials for studies abroad and prioritizes national interests. Poorer countries currently lacking their own genomics initiatives could benefit from similar legislation balancing the protection of “genomic sovereignty” while fostering international collaborations that bring much-needed resources and increase local scientific capacity. Beyond the improvement of their basic genomics research capabilities, governments should engage their relevant ministries to develop a plan to integrate genetic and genomics products (including diagnostics, vaccines, therapies, and others), within the health system and public health programs with emphasis on accessibility and equity to improve health for all. A good example of priority setting in genomics is Mexico’s national genomics program over the last 15 years (see Box 2).

To strengthen genomics globally, the tools necessary for analysis of genomics data are urgently needed in developing countries, where they are currently underutilized [43]. A problem with genomics is that much of the advanced knowledge is concentrated in individuals and a few research centers and companies rather than in textbooks or academia, restricting dissemination even though massive amounts of genomic data and software are openly accessible through the Internet. A conscious effort on the part of developed nations to transfer their knowledge of the use and analysis of genomic databases needs to be encouraged to help developing countries manage their own specific data on indigenous biological species, local epidemiology and infectious diseases, biodiversity, and other issues. Some successful programs and initiatives include the Wellcome Trust Sanger Institute training courses on bioinformatics and genomic analysis, the Sustainable Sciences Institute–Broad Institute bioinformatics workshops (Figure 1), and the TDR/WHO-South African Bioinformatics Institute (SANBI) regional training center. Online training like the S-star alliance bioinformatics courses and conferences such as the African Bioinformatics Conference (Afbix’09) with remote participation are becoming more widespread and are an excellent option for countries with limited resources. GARSA (Genomic Analysis Resources for Sequence Annotation) is a flexible Web-based system designed to analyze genomic data in the context of a data analysis pipeline. Hosted in Brazil, this free system aims to facilitate the analysis, integration, and presentation of genomic information, concatenating several bioinformatics tools and sequence databases with a simple user interface [44]. An alternative to on-site sequencing is to partner with colleagues in more-developed countries to have samples processed abroad in sequencing centers. This is possible only if local legislation allows for export of biological samples, and if true partnership and trust exist with a colleague(s) in the developed country.

As developing countries reevaluate their role in the genomics era, they will continue to explore the unique opportunities that arise from the vast natural and genomic diversity that they embody. As exemplified by the successes in Brazil, Mexico, and several African countries, it is possible to turn challenges and problems such as emerging and endemic infectious diseases into opportunities for unique scientific and economic growth. Access to sequencing facilities, open-source databases, and harmonized methodologies for genomic analysis are essential for the future of genomics in the developing world. However, unless a more concerted effort is made to include countries with limited scientific development and resources, it is unlikely that they will fully participate in genomics projects or use the technologies available other than by allowing their genetic material to be accessible to others. As emerging countries set their own priorities for genomics research and take ownership of its results, the main challenge across developing nations remains access to training and knowledge translation. Human resources and local capacity in genomics are thus central to development, as countries with these skills could participate in the potential benefits of the field with respect to health, food security, natural resource management, and other critical areas. “North–South” and “South–South” collaborations are a viable and extremely rewarding way to increase the capacities of developing countries to access genomic tools to address unique problems considered of little economic value outside these countries but of tremendous importance to the majority of the world’s population.



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