Abstract
Personalized medicine is strongly tied with human variome research: understanding the impact of specific genetic sequence mutations on observable human traits will play a key role in the quest for custom drugs therapies and improved patient care. Recent growth in this particular field leveraged the appearance of locus-specific databases (LSDBs). Although these systems are praised in the scientific community, they lack some features that can promote a more widespread usage. Existing systems are closed, independent and designed solely for gene curators. In this paper we present a new approach based on a holistic perspective of the genomic variation field, envisaging the integration of LSDBs, genes and variants, as well as a broad set of related resources in an innovative workspace. A prototype implementation for this approach is deployed online at http://bioinformatics.ua.pt/WAVe .
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Watson, J.D.: The human genome project: past, present, and future. Science 248, 44–49 (1990)
Bottinger, E.P.: Foundations, promises and uncertainties of personalized medicine. Mount Sinai Journal of Medicine: A Journal of Translational and Personalized Medicine 74, 15–21 (2007)
Ginsburg, G.S., McCarthy, J.J.: Personalized medicine: revolutionizing drug discovery and patient care. Trends in Biotechnology 19, 491–496 (2001)
Ring, H.Z., Kwok, P.-Y., Cotton, R.G.: Human Variome Project: an international collaboration to catalogue human genetic variation. Pharmacogenomics 7, 969–972 (2006)
Cotton, R.G.H.: Recommendations of the 2006 Human Variome Project meeting. Nature Genetics 39, 433–436 (2007)
Fokkema, I.F.A.C., den Dunnen, J.T., Taschner, P.E.M.: LOVD: Easy creation of a locus-specific sequence variation database using an ldquoLSDB-in-a-boxrdquo approach. Human Mutation 26, 63–68 (2005)
Béroud, C., Collod-Béroud, G., Boileau, C., Soussi, T., Junien, C.: UMD (Universal Mutation Database): A generic software to build and analyze locus-specific databases. Human Mutation 15, 86–94 (2000)
Riikonen, P., Vihinen, M.: MUTbase: maintenance and analysis of distributed mutation databases. Bioinformatics 15, 852–859 (1999)
Thorisson, G.A., Muilu, J., Brookes, A.J.: Genotype-phenotype databases: challenges and solutions for the post-genomic era. Nat. Rev. Genet. 10, 9–18 (2009)
Lopes, P., Arrais, J., Oliveira, J.L.: Link Integrator - A Link-based Data Integration Architecture. In: Fred, A.L.N. (ed.) International Conference on Knowledge Discovery and Information Retrieval, pp. 274–277. INSTICC Press, Funchal - Madeira (2009)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Lopes, P., Luís Oliveira, J. (2012). A Holistic Approach for Integrating Genomic Variation Information. In: Freitas, A.T., Navarro, A. (eds) Bioinformatics for Personalized Medicine. JBI 2010. Lecture Notes in Computer Science(), vol 6620. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-28062-7_5
Download citation
DOI: https://doi.org/10.1007/978-3-642-28062-7_5
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-28061-0
Online ISBN: 978-3-642-28062-7
eBook Packages: Computer ScienceComputer Science (R0)