Abstract
Information about small genetic variations in organisms, known as single nucleotide polymorphism (SNPs), is crucial to identify candidate genes that have a role in disease susceptibility, a long-standing research goal in biology. While a number of established public SNP databases are available, the specification of effective techniques for SNP analysis remains an open issue. We describe a secondary SNP database that integrates data from multiple public sources, designed to support various experimental ranking models for SNPs. By prioritizing SNPs within large regions of the genome, scientists are able to rapidly narrow their search for candidate genes. In the paper we describe the ranking models, the data integration architecture, and preliminary experimental results.
This is a preview of subscription content, log in via an institution to check access.
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Chakravarti, A.: Population genetics – making sense out of sequence. Nature Genetics, 21(Suppl. 1) (January 1999)
Conde, L., Vaquerizas, J.M., Dopazo, H., Arbiza, L.: PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res 34, W621–W625 (2006)
Coulet, A., Smaïl-Tabbone, M., Benlian, P., Napoli, A., Devignes, M.: SNP-Converter: An ontology-based solution to reconcile heterogeneous SNP descriptions for pharmacogenomic studies. In: Leser, U., Naumann, F., Eckman, B.A. (eds.) DILS 2006. LNCS (LNBI), vol. 4075, pp. 82–93. Springer, Heidelberg (2006)
Eppig, J.T., Blake, J.A., Bult, C.J., Kadin, J.A., Richardson, J.E.: The Mouse Genome Database Group. The mouse genome database (MGD): new features facilitating a model system. Nucl. Acids Res. 35(Database issue), D630–D637 (2007)
Hubbard, T.J.P., Aken, B.L., Beal, K., et al.: Ensembl 2007. Nucl. Acids Res 35(suppl_1), D610–D617 (2007)
Hull, D., Wolstencroft, K., Stevens, R., Goble, C., Pocock, M., Li, P., Oinn, T.: Taverna: a tool for building and running workflows of services. Nucl. Acids Res. 34(Web Server issue), W729–W732 (2006)
Jegga, A.G., Gowrisankar, S., Chen, J., Aronow, B.J.: PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease. Nucleic Acids Res. 35,D700–D706 (2007)
Kuhn, R.M., Karolchik, D., Zweig, A.S., Trumbower, H., et al.: The UCSC genome browser database: update 2007. Nucl. Acids Res. 35(Database issue), D668–D673 (2007)
Reumers, J., Maurer-Stroh, S., Schymkowitz, J., Rousseau, F.: SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs. Bioinformatics 22(17), 2183–2185 (2006)
Reuveni, E., Ramensky, V.E., Gross, C.: Mouse SNP miner: An annotated database of mouse functional single nucleotide polymorphism. BMC Genomics 8(24) (2007)
Riva, A., Kohane, I.S.: SNPper: retrieval and analysis of human SNPs. Bioinformatics 18(12), 1681–1685 (2002)
Wang, L., Liu, S., Niu, T., Xu, X.: SNPHunter: a bioinformatic software for single nucleotide polymorphism data acquisition and management. BMC Bioinformatics 6(60), (2005) doi:10.1186/1471-2105-6-60
Wang, P., Dai, M., Xuan, W., McEachin, R.C., Jackson, A.U., Scott, L.J., Athey, B., et al.: SNP function portal: a web database for exploring the function implication of SNP alleles. Bioinformatics 22(14), e523–e529 (2006)
Wheeler, D.L., Barrett, T., Benson, D.A., Bryant, S.H.: Database resources of the national center for biotechnology information. Nucl. Acids Res. 35(Database issue), D5–D12 (2007)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2007 Springer Berlin Heidelberg
About this paper
Cite this paper
Missier, P., Embury, S., Hedeler, C., Greenwood, M., Pennock, J., Brass, A. (2007). Accelerating Disease Gene Identification Through Integrated SNP Data Analysis. In: Cohen-Boulakia, S., Tannen, V. (eds) Data Integration in the Life Sciences. DILS 2007. Lecture Notes in Computer Science(), vol 4544. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-73255-6_18
Download citation
DOI: https://doi.org/10.1007/978-3-540-73255-6_18
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-73254-9
Online ISBN: 978-3-540-73255-6
eBook Packages: Computer ScienceComputer Science (R0)