Pcbi.1000115 1.8

Outlook on Thailand’s Genomics and ComputationalBiology Research and Development Wannipha Tongsima1, Sissades Tongsima2, Prasit Palittapongarnpim1,3* 1 National Science and Technology Development Agency (NSTDA), Pathumtani, Thailand, 2 National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathumthani, Thailand, 3 Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand capacity building through infrastructure/ priority technological disciplines. There- fore, the applications of both disciplines in biomedical and agricultural research have tradition of agriculture-based industries, been enthusiastically endorsed and finan- Investment (BOI) promotes foreign invest- tive location for life sciences investment.
porate tax exemption for up to eight years.
Thailand’s unique ecosystems are locat- ment include bioinformatics solution ser- temperate north, the rich central plain, the grove forests along the coastal areas. The established the Thailand Center of Excel- agriculture, food processing, and biomed- opment in life sciences business by creat- ing partnerships with foreign investors. To foster biotechnology industries. In 2002, crease Thailand’s participation in bioin- government as well as from other business- (northern vicinity of Bangkok). To support related sources. To protect the investment infrastructure, education, and sustainable also promotes legal protection of science bioinformatics research activity and rec- Thailand’s first BioPark within the Thai- creased research activity involving geno- such as organization of the first Interna- was established to create opportunities to recognized by the country’s leaders as key applications in some specific local areas.
However, the applications to other impor-tant areas, such as agriculture, are ham- Citation: Tongsima W, Tongsima S, Palittapongarnpim P (2008) Outlook on Thailand’s Genomics and pered by the limited availability of geno- Computational Biology Research and Development. PLoS Comput Biol 4(7): e1000115. doi:10.1371/journal.
necessary biochemical/physiological infor- Editor: Philip E. Bourne, University of California San Diego, United States of America more genomic information in publicdatabases, Thailand’s research community Copyright: ß 2008 Tongsima et al. This is an open-access article distributed under the terms of the CreativeCommons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, is striving to adopt comparative genomics provided the original author and source are credited.
to obtain information of direct relevance Funding: The authors are all employees of BIOTEC, NSTDA. PP is also an employee of Mahidol University.
Competing Interests: All authors are employees of the National Science and Technology Development needs. This article highlights Thailand’s Agency (NSTDA). ST works for BIOTEC, which is one of the national centers under NSTDA. WT and PP are employed directly by NSTDA. PP is also an employee of Mahidol University. PP and WT are former employees of matics in the following areas: (1) policy PLoS Computational Biology | www.ploscompbiol.org July 2008 | Volume 4 | Issue 7 | e1000115 of distinguished speakers, including Dr.
Carlos Morel, the Director of the special US$1.7 million to improving bioinformatic and genomic computing infrastructures.
Health Organization (WHO) at the time.
His influential role succeeded in persuad- Institute, investing US$2.5 million for a state-of-the-art pyrosequencer, called 454 scientific community to realize the impor- tance of genomics and bioinformatics. Dr.
desorption/ionization time-of-flight mass described above, there are still few Thai tion of local computer scientists the need researchers in this field. Currently, 40 or genomics and bioinformatics will facilitate the cash-starved research on tropical and various fields, e.g., mathematics, chemistry, strated how useful bioinformatics is, espe- neglected diseases, TDR–WHO initiated a computer sciences, and biology, work in the program in 2003 to further bioinformatics the success of this meeting, and with AP- biology. The majority of these researchers on the condition that the graduates return to work in Thailand, and it is expected that University, (http://www.ssi-tdr.net/cbag/), is one of the centers that provides regular training courses by instructors from many biology in the next five years. In the future, renowned institutes around the world. Upon the completion of the training, the local programs in bioinformatics will be offered trainees are expected to use the knowledge ture, (3) supporting bioinformatic educa- subsections discuss the last three supports an introductory online course on bioinfor- matics, distributed through an e-learning researchers from various institutions for throughout the country. Thai universities and systems biology. This section discusses into various graduate-level curricula in life University’s Genome Informatics Lab). The sciences. Hence, this activity could jump- generation and utilization of genomic data Bio-Mirror in Thailand (http://bio-mirror.
start bioinformatic education in Thailand, ku.ac.th) aims to provide local access to where local bioinformatics experts are still various public databases, e.g., GenBank.
Currently, the networking infrastructure has been dramatically improved with two major come available, more universities will start national research institutes. In 2006, the ed the first Master’s program in Thailand (SIPA), under the Ministry of Information Southeast Asia. It is responsible for 20% of www.bioinformatics.kmutt.ac.th/course.
acquired septicemia cases in northeastern US$1.5 million for the installation of the php). This Master’s program accepts 10– largest computational grid infrastructure in 15 students per year from a wide range of fatality rate. In 1998, the 7.25 Mb genome Thailand to support all kinds of research in of B. pseudomallei K96243 was sequenced by a research team at the Wellcome Trust Sanger national or international research insti- Institute, with significant contribution from Dr. Sirirurg Songsivilai, Mahidol University performance computers (HPC) since 2002.
[2]. The relatively large genome contains 16 genomic islands that together make up 6.1% research institutes, while some have pur- performance of seven terra floating point sued doctoral degrees abroad in bioinfor- organisms such as B. mallei and may account PLoS Computational Biology | www.ploscompbiol.org July 2008 | Volume 4 | Issue 7 | e1000115 for the clinical features of melioidosis caused by the organism. More information and the ject aims to increase understanding of this organism’s metabolic and regulatory path- bacterium were recently reported [3].
ment of Spirulina for commercial purposes.
The project is in the finishing steps, and the results should soon be available to the tioned SNP studies as well as from large- data, efforts were made by Thai researchers scale SNP genotyping projects (see http:// this news event, the Thai press stimulated to apply the information to improve medical public interest in genomics and bioinfor- lows search for Thai-specific SNPs as well matics, leading to greater public awareness of the feasibility and potential of these two population or not. A collaborative project searchers sequenced two million base pairs Institut Pasteur, and the Centre National different populations can be displayed in a de Ge´notypage (CNG) [14] in Evry, France, comparative view illustrating the underly- fostered the ability of Thai researchers to Thai population and design specific prim- ers to genotype such SNPs. To assist this sequencing cost over the past few years has whose profiles fit the selection criteria). As specific primers [16] as well as resequen- questions. Avian influenza was inevitably database. The novel SNPs, however, tend to the rest of the world, and to help solve the have allele frequencies less than 5%) and recent dispute regarding the sharing of the viral samples between the affected devel- genome-wide SNP allele frequencies of the association studies. Most of them utilized vaccines or drugs, and for monitoring the genome resequencing project at this point influenza virus. The sequence information would still be exorbitant. In the near future, array. The first of such studies, funded by the genetic determinants that would affect the severity of b-thalassemia/HbE diseases, nese and Japanese. The Thai population is Mahidol University, in collaboration with likely to be more diverse in origin and has vides insight into the evolution of these a significant additional genetic relationship with the Indian population, among others.
disorder in Southeast Asia, manifested as standing of infectious diseases. For exam- partment of Medical Sciences, Ministry of caused by a combination of genetic variants.
virus type I collected over a 30-y period revealed the associations between genetic patients with either mild or severe symptoms prevalence, and decline in serotype prev- study the transferability (from the Japanese population to the Thai population) of 861 severity have been identified and are being verified. Allele frequencies across a large individuals from four regions in Thailand (north, central, northeast, and south). It regional populations are generally similar to each other and to the Japanese htSNPs.
affecting the severity of osteoporosis. This PLoS Computational Biology | www.ploscompbiol.org July 2008 | Volume 4 | Issue 7 | e1000115 antimicrobial peptides [22], host–defense provided allele frequency of a different set related genes [23], fortilin [24,25], and sex-related genes [26], were reported. The identify genes associated with adverse drug research institutes around the world.
reactions to nevirapine, which is one of the metabolic and regulatory network profiles reconstruct a biological system from mis- aquatic invertebrates, including other spe- nevirapine, zidovudine, and lamivudine.
cies of shrimps, lobsters, and crabs.
National List of Essential Medicines.
However, adverse drug reactions, particu- where it is a major source of animal feed as larly in the form of drug rash, occur very pathways of malaria and tuberculosis [44].
scribed individuals. The potentially lethal reactions would inevitably force the people to use much more expensive drugs [17]. In ESTs from 12 leaf and root libraries.
control of 80 individuals without drug rash phoresis is an established experimental tool in several Thai laboratories and has been fied as clinically useful predictors of such used to identify plant and animal proteins expressed in various conditions, including ‘‘wet’’ laboratory experiments.
cassava, peanut, shrimp [28], and microbes, with post-traumatic stress disorder found satellites, or numerous short segments of malarial parasites. Proteomic analysis has also been applied to biomedical research on should be noted that this was one of those manifestations can be associated with micro- rare occasions in which a large number of cholangiocarcinoma cell line [32,33], but people were simultaneously exposed to the in the main on urinary samples. It is hoped tandem repeat in the nitric oxide synthase that proteomic profiling of urine will lead to better understanding of renal physiology, severe malaria in Thailand [45]. Microsatel- lites are also exploited to identify genetic targeting other medical-related projects, relationships for forensic applications.
including leprosy, leukemia, hepatocellular particularly useful in identifying protein that is linked to a gene locus of interest, depletion, a condition that leads to skeletal, (SSR) marker, is used to assist selective tags (ESTs) are studied to identify genes breeding programs. Marker-assisted selec- relatively common among Thais [35,36].
laborious phenotypic testing. It also allows selection at an early stage of growth before the phenotype of interest is observable.
is not yet completely sequenced, as in the can still be discovered from EST sequenc- such as eye, leukocyte, testis, and ovary.
sugarcane (Saccharum L.), peanut (Arachis as microsatellites [21] and SNPs have been hypogaea L.), oil palm (Elaeis guineensis, discovered. Some important genes, such as Jacq.), soybean (Glycine max Merr.) [46], PLoS Computational Biology | www.ploscompbiol.org July 2008 | Volume 4 | Issue 7 | e1000115 and rubber tree (Hevea brasiliensis Muell.
that are amenable to formulation of target- Arg.) [47]. It is anticipated that these and hepatitis B patients, respectively [59,60].
logical step is to identify drug candidates.
18 level [61] and the methylation status of Conventionally, this is done by screening proteins or target organisms. The hit rate is usually low. Therefore, a large library of cancer patients is of particular interest microbes. Early Thai research efforts led treatment should be, while minimizing the side effects. Similar studies have, therefore, of Mycobacterium tuberculosis [48], which been done with other cancers. Markers for were later shown to be useful markers for long-term survival have been identified for bacterial species, including Escherichia coli, cancer, a mutation associated with recur- Salmonella, Shigella, Vibrio cholerae, Leptospira, with possible inhibitory activity against the logical studies is being evaluated [50].
are being validated in Thai laboratories.
dubbed ‘‘RiceGeneThresher’’ (http://rice.
malaria. Most antibiotics bind specifically to target proteins and disrupt their functions, Plasmodium, are particularly fruitful, as leading to bacterial cell death or growth arrest. Current antibiotic targets include this research is exemplified by the recent Postgenomic research has begun to identify derivatives that inhibit this enzyme [73].
genes associated with agronomic traits such A similar strategy has also been applied to other microbes, namely M. tuberculosis and brown planthopper (Nilaparvata lugens Stal) resistance [55], leaf and neck blast resistance [56], and other traits [57]. The most notable prized as a national asset. Genetic markers trained scientists in the field of genomics thymidylate synthase, an enzyme naturally tolerance have been filed for international able to keep up with the advances in life patents, and can be utilized for rice breeding research and development utilizing bioin- formatics is needed to solve local agricul- other genomic platforms should be able to the core processes of life [68], a number of provide universal health coverage for all genes likely to be essential for M. tubercu- losis have been identified. Among them, 47 occurrence or progression of diseases are needed to minimize the cost of health care.
them theoretically safe as drug targets.
tational biologists so that they can share discovery of various biomarkers, although the clinical usefulness of most of them is fructose-1, 6-bisphosphate aldolase. Com- agricultural biotechnology is particularly yet to be confirmed. Hepatitis B infection pounds known to inhibit the enzymes in E.
coli, as well as their derivatives, were tested sequence data and basic biological infor- against M. tuberculosis. One compound, 5- mation on agriculturally important organ- cellular carcinoma (HCC), a liver cancer, be active against laboratory and clinical uncovered SNPs in the interleukin-18 (IL- developing countries is, therefore, to make PLoS Computational Biology | www.ploscompbiol.org July 2008 | Volume 4 | Issue 7 | e1000115 inferences about organisms of local inter- Wannipha Tongsima, M.S., obtained her master’s degree in Industrial Microbiology from Chulalongkorn University, Thailand. She was involved infounding the Bioinformatics research program in BIOTEC. To reinforce the The authors would like to acknowledge the research activity in this area, she also helped organize the first International editor and referee(s) for their useful comments Conference on Computational Biology (InCoB), held in Bangkok in 2002. Later, she which improved this paper. We also thank the was appointed to manage one of the first BIOTEC ethnic-specific human genetic writing clinic team, particularly Drs. PhillipShaw and Nitsara Karoonuthaisiri at BIOTEC, variation programs, named the Thailand SNP Discovery Project. She works as a for giving us extremely helpful comments to Genomic Medicine program coordinator for the Cluster and Program Manage- ment Office (CPMO) of the National Science and Technology DevelopmentAgency (NSTDA), which is an umbrella organization of four other national research centers in Thailand, including BIOTEC.
Sissades Tongsima, Ph.D., received his doctoral degree in Computer Science and Engineering from the University of Notre Dame, Indiana, United States. Hehas worked for the National Electronics and Computer Technology Center onHigh Performance Computing (HPC) and Computational Grid. During 2002–2004,he cochaired the Asia-Pacific Advanced Network (APAN) Grid Working Group. In2003, he shifted his research direction from HPC architecture to bioinformaticsresearch, when he started working for BIOTEC, and constructed the ThaiSNPdatabase. His main research interest is in developing algorithms and databasesfor analyzing various research projects on human genetic variation. He currentlyheads the Genome Institute biostatistics and informatics laboratory at BIOTEC.
Prasit Palittapongarnpim, M.D., earned his medical degree from MahidolUniversity, Thailand, and his B.S. in Mathematics from Ramkumhang University,Thailand. He is a Fellow of the Royal College of Pediatricians of Thailand and alsoan Associate Professor in Microbiology at Mahidol University, where he hasconducted research focusing on tuberculosis. While holding a Deputy Directorposition, he initiated the Bioinformatics research program at BIOTEC in 2002 andled the organization of the first InCoB conference in 2002. He is currently a VicePresident of NSTDA.
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Source: http://www4a.biotec.or.th/GI/publications/bsi/journal.pcbi.1000115.pdf