Bioinformatics: Towards New Directions for Public Health^[*]

Summary

Objectives: Epidemiologists are reformulating their classical approaches to diseases by considering various issues associated to “omics” areas and technologies. Traditional differences between epidemiology and genetics include background, training, terminologies, study designs and others. Public health and epidemiology are increasingly looking forward to using methodologies and informatics tools, facilitated by the Bioinformatics community, for managing genomic information. Our aim is to describe which are the most important implications related with the increasing use of genomic information for public health practice, research and education. To review the contribution of bioinformatics to these issues, in terms of providing the methods and tools needed for processing genetic information from pathogens and patients. To analyze the research challenges in biomedical informatics related with the need of integration of clinical, environmental and genetic data and the new scenarios arisen in public health.

Methods: Review of the literature, Internet resources and material and reports generated by internal and external research projects.

Results: New developments are needed to advance in the study of the interactions between environmental agents and genetic factors involved in the development of diseases. The use of biomarkers, biobanks, and integrated genomic/clinical databases poses serious challenges for informaticians in order to extract useful information and knowledge for public health, biomedical research and healthcare.

Conclusions: From an informatics perspective, integrated medical/biological ontologies and new semantic-based models for managing information provide new challenges for research in areas such as genetic epidemiology and the “omics” disciplines, among others. In this regard, there are various ethical, privacy, informed consent and social implications, that should be carefully addressed by researchers, practitioners and policy makers.

Keywords

Public health - bioinformatics - epidemiology - genomics - medical informatics

^* This paper is based on our invited review paper that appeared in: Haux R, Kulikowski E (eds.). IMIA Yearbook of Medical Informatics 2004: Towards Clinical Informatics. Stuttgart: Schattauer 2004; pp. 137-43.

• References

• 1 Butler D. Epidemiology set to get fast-track treatment. Nature 2001; 414 6860 139
• 2 Maojo V, Kulikowski CA. Bioinformatics and Medical Informatics: Collaboration on the Road to Genomic Medicine? JAMIA 2003 (in press).
• 3 Perera FP, Weinstein IB. Molecular epidemiology: recent advances and future directions. Carcinogenesis 2000; 21 (03) 517-24.
• 4 Furberg AH, Ambrosone CB. Molecular epidemiology, biomarkers and cancer prevention. Trends Mol Med 2001; 7 (11) 517-21.
• 5 Lilienfeld AM, Lilienfeld DE. The 1979 Health Clark lectures. ‘The epidemiologic fabric’. I – Weaving the threads. Int J Epidemiol 1980; 9 (03) 199-206.
• 6 Potter JD. At the interfaces of epidemiology, genetics and genomics. Nat Rev Genet 2000; 2 (02) 142-7.
• 7 Foxman B, Riley L. Molecular epidemiology: focus on infection. Am J Epidemiol 2001; 153 (12) 1135-41.
• 8 Beskow LM, Khoury MJ, Baker TG, Thrasher JF. The Integration of Genomics into Public Health Research, Policy and Practice in the United States. Community Genet 2001; 4 (01) 2-11.
• 9 Maojo V, Iakovidis I, Martin-Sanchez F, Crespo J, Kulikowski C. Medical informatics and bioinformatics: European efforts to facilitate synergy. J Biomed Inform 2001; 34 (06) 423-7.
• 10 Martin-Sanchez F, Maojo V, Lopez-Campos G. Integrating genomics into health information systems. Methods Inf Med 2002; 41 (01) 25-30.
• 11 Collins FS, McKusick VA. Implications of the Human Genome Project for medical science. JAMA 2001; 285 (05) 540-4.
• 12 Collins FS, Guttmacher AE. Genetics moves into the medical mainstream. JAMA 2001; 286 (18) 2322-4.
• 13 Kohane I. Bioinformatics and Clinical Informatics: The Imperative to Collaborate. JAMIA 2000; 7 (05) 439-43.
• 14 Kulikowski C. The Micro-Macro Spectrum of Medical Informatics. Challenges: From Molecular Medicine to Transforming Health Care in a Globalizing Society. Methods Inf Med 2001; 41: 20-4.
• 15 Miller P. Opportunities at the Intersection of Bioinformatics and Health Informatics. JAMIA 2000; 7 (05) 431-8.
• 16 Altman R. The Interactions Between Clinical Informatics and Bioinformatics. JAMIA 2000; 7 (05) 439-43.
• 17 Henry CJ, Phillips R, Carpanini F, Corton JC, Craig K, Igarashi K, Leboeuf R, Marchant G, Osborn K, Pennie WD, Smith LL, Teta MJ, Vu V. Use of genomics in toxicology and epidemiology: findings and recommendations of a workshop. Environ Health Perspect 2002; 110 (10) 1047-50.
• 18 Benton D. Bioinformatics – principles and potential of a new multidisciplinary tool. Trends Biotechnol 1996; 14 (08) 261-72.
• 19 Roberts RJ. The early days of bioinformatics publishing. Bioinformatics 2000; 16 (01) 2-4.
• 20 Bairoch A. Serendipity in bioinformatics, the tribulations of a Swiss bioinformatician through exciting times! Bioinformatics. 2000; 16 (01) 48-64.
• 21 Mount D. Bioinformatics: Sequence and Genome Analysis. Cold Spring Harbor Laboratory. Cold Spring Harbor; NY: 2001
• 22 van Belkum A, Struelens M, de Visser A, Verbrugh H, Tibayrenc M. Role of genomic typing in taxonomy, evolutionary genetics, and microbial epidemiology. Clin Microbiol Rev 2001; 14 (03) 547-60.
• 23 Dalma-Weiszhausz DD, Chicurel ME, Gingeras TR. Microarrays and Genetic Epidemiology: A Multipurpose Tool for a Multifaceted Field. Genetic Epidemiology 2002; 23: 4-20.
• 24 Lander ES. et al. Initial sequencing and analysis of the human genome. Nature 2001; 409 6822 860-921.
• 25 Olden K, Wilson S. Environmental health and genomics: visions and implications. Nat Rev Genet 2000; 1 (02) 149-53.
• 26 Fauci AS. Infectious diseases: considerations for the 21st century. Clin Infect Dis 2001; 32 (05) 675-85.
• 27 Pang T. The impact of genomics on global health. Am J Public Health 2002; 92 (07) 1077-9.
• 28 Austin MA. Ethical issues in human genome epidemiology: a case study based on the Japanese American Family Study in Seattle, Washington. Am J Epidemiol 2002; 155 (07) 585-92.
• 29 Khoury M, Little J, Burke W. Human Genome Epidemiology: A scientific foundation for using genetic information to improve health and prevent disease. New York: Oxford University Press; 2004
• 30 Annas GJ. Rules for research on human genetic variation – lessons from Iceland. N Engl J Med 2000; 342 (24) 1830-3. Epidemiol 2002; 155 (7) 585-92
• 31 Cambon-Thomsen A. Assessing the impact of biobanks. Nat Genet 2003; 34 (01) 25-6.
• 32 Kaiser J. Biobanks. Population databases boom, from Iceland to the U.S. Science 2002; 298 5596 1158-61.
• 33 Ellsworth DL, Manolio TA. The Emerging Importance of Genetics in Epidemiologic Research III. Bioinformatics and statistical genetic methods. Ann Epidemiol 1999; 9 (04) 207-24.
• 34 Institute of Medicine. The Future of Public Health. Washington, DC: National Academy Press; 1988
• 35 Steinberg KK, Gwinn M, Khoury MJ. The role of genomics in public health and disease prevention. JAMA 2001; 286 (13) 1635
• 36 Weatherall D. Science and the Quiet Art. Medical Research & Patient Care. Oxford: Oxford University Press; 1995
• 37 Noonan AS. Integrating genomics into US public health. Genet Med 2002; 4 (Suppl. 06) Suppl 68S-71S.
• 38 Mostowy S, Behr MA. Comparative genomics in the fight against tuberculosis: diagnostics, epidemiology, and BCG vaccination. Am J Pharmacogenomics 2002; 2 (03) 189-96.
• 39 Schork NJ, Fallin D, Lanchbury JS. Single nucleotide polymorphisms and the future of genetic epidemiology. Clin Genet 2000; 58 (04) 250-64.
• 40 Hoffman SL. Infectious disease. Research (genomics) is crucial to attacking malaria. Science 2000; 290 5496 1509
• 41 Musen M, van Bemmel JH. Challenges for Medical Informatics as an Academic Discipline. Methods Inf Med 2002; 41: 1-3.
• 42 Genkin A, Kulikowski CA, Muchnik I. Set covering submodular maximization: An optimal algorithm for data mining in bioinformatics and medical informatics. Journal of Intelligent and Fuzzy Systems 2002; 12 (01) 5-17.
• 43 Maojo V, Crespo J. Challenges for future intelligent systems in biomedicine. Journal of Intelligent and Fuzzy Systems 2002; 12 (01) 1-3.
• 44 Ohno-Machado L, Vinterbo SA, Weber G. Classification of gene expression data using fuzzy logic. Journal of Intelligent and Fuzzy Systems 2002; 12 (01) 19-24.
• 45 Gruber TR. A Translation Approach to Portable Ontology Specifications, Knowledge Acquisition. 1993; 5 (02) 199-220.
• 46 Pérez-Rey D, Maojo V, García-Remesal M, Alonso-Calvo R. Biomedical ontologies in post-genomic information systems. Proceedings of IEEE Fourth Symposium on Bioinformatics and Bioengineering. Taichung, Taiwan. 2004. (in press)
• 47 McGuinness D, van Harmelen F. OWL (Web Ontology Language). Overview, W3C Recommendation. February 10. 2004. www.w3.org/TR/2004/REC-owl-features-20040210/
• 48 García-Remesal M, Maojo V, Billhardt H, Crespo J, Alonso-Calvo R, Pérez-Rey D, Martín F, Sousa A. ARMEDA II: Supporting Genomic Medicine through the Integration of Medical and Genetic Databases. Proceedings of the IEEE Fourth Symposium on Bioinformatics and Bioengineering (BIBE 2004), T’aichung (Taiwan-ROC). May. 2004. (in press)
• 49 Silvescu A, Reinoso-Castillo J, Honavar V. Ontology-Driven information extraction and knowledge acquisition from heterogeneous, distributed, autonomous biological data sources. Proceedings of the IJCAI2001 Workshop on Knowledge Discovery from Heterogeneous, Distributed, Autonomous, Dynamic Data and Knowledge Sources. 2001
• 50 Köhler J, Philippi S, Lange M. SEMEDA: ontology based semantic integration of biological databases. Bioinformatics 2003; 19 (18) 2420-7.
• 51 The Gene Ontology Consortium. Gene Ontology: tool for the unification of biology. Nature Genetics 2000; 25: 25-9.
• 52 Bertone P, Gerstein M. Integrative data mining: the new direction in bioinformatics. IEEE Eng Med Biol Mag 2001; 20 (04) 33-40.
• 53 Gilbert GL. Molecular diagnostics in infectious diseases and public health microbiology: cottage cottage industry to postgenomics. Trends Mol Med 2002; 8 (06) 280-7.
• 54 Broder S, Hoffman SL, Hotez PJ. Cures for the Third World’s problems: the application of genomics to the diseases plaguing the developing world may have huge medical and economic benefits for those countries and might even prevent armed conflict. EMBO Rep 2002; 3 (09) 806-12.
• 55 Goldie SJ, Levin AR. Genomics in medicine and public health: role of cost-effectiveness analysis. JAMA 2001; 286 (13) 1637-8.
• 56 Visionary experimental designs. Nature 2001; 414 6860 133 [No authors listed]
• 57 Millikan R. The changing face of epidemiology in the genomics era. Epidemiology 2002; 13 (04) 472-80.
• 58 Maojo V, Martin-Sanchez F, Billhardt H, Iakovidis I, Kulikowski C. Establishing an agenda for biomedical informatics. Methods Inf Med 2003; 42 (02) 121-5.
• 59 Martin-Sanchez F. et al. Synergy between research in Medical Informatics and Bioinformatics: facilitating genomic medicine for future healthcare. J Biomed Inform 2004; 37 (01) 30-42.