Two birds, one stone: Selecting functionally informative tag SNPs for disease association studies

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4645 LNBI, Issue , 2007, Pages 61-72

  Lee, Phil Hyoun ^a   Shatkay, Hagit ^a  

^a QUEEN S UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CHARACTERIZATION; DATABASE SYSTEMS; GENES; HEURISTIC ALGORITHMS; MULTIOBJECTIVE OPTIMIZATION; PROBLEM SOLVING;

DATASETS; FUNCTIONAL EFFECTS; GENOMIC REGIONS;

DISEASES;

EID: 37249021845     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-74126-8_7     Document Type: Conference Paper

References (33)

1. Hedrick, P.: Genetics of pouplation, 3rd edn. Jones and Bartlett Publishers (2004)
2. Bhatti, P., Church, D., Rutter, J.L., Struewing, J.P., Sigurdson, A.J.: Candidate single nucleotide polymorphism selection using publicly available tools: a guide for epidemiologists. American Journal of Epidemiology 164, 794-804 (2006)
3. Sherry, S., Ward, M., Kholodov, M., Baker, J., Phan, L., Smigielski, E., Sirotkin, K.: dbSNP: the NCBI database of genetic variation. Nucleic Acids Research 29, 308-311 (2001)
4. Brunham, L.R., Singaraja, R.R., Pape, T.D., Kejariwai, A., Thomas, P.D., Hayden, M.R.: Accurate prediction of the functional significance of single nucleotide polymorphisms and mutations in the ABCA1 gene. PLOS Genetics 1, 739-747 (2005)
5. Rebbeck, T.R., Ambrosone, C.B., Bell, D.A., Chanock, S.J., Hayes, R.B., Kadlubar, F.F., Thomas, D.C.: SNPs, haplotypes, and cancer: applications in molecular epidemiology. Cancer Epidemiology, Biomarkers & Prevention 13, 681-687 (2004)
6. Conde, L., Vaquerizas, J.M., Ferrer-Costa, C., de la Cruz, X., Orozco, M., Dopazol, J.: PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes. American Journal of Epidemiology 33, W501-W505 (2005)
7. Hemminger, B.M., Saelim, B., Sullivan, RF.: TAMAL: an integrated approach to choosing SNPs for genetic studies of human complex traits. Bioinformatics 22, 626-627 (2006)
8. Xu, H., Gregory, S.G., Hauser, E.R., Stenger, J.E., Pericak-Vance, M.A., Vance, J.M., Zuchner, S., Hauser, M.A.: SNPselector: a web tool for selecting SNPs for genetic association studies. Bioinformatics 21, 4181-4186 (2005)
9. Lee, P.H., Shatkay, H.: BNTagger: improved tagging SNP selection using Bayesian networks. Bioinformatics 22, e211-219 (2006)
10. Sebastiani, P., Lazarus, R., Weiss, S.T., Kunkel, L.M., Kohane, I.S., Ramoni, M.F.: Minimal haplotype tagging. Proceedings of the National Academy of Sciences 100, 9900-9905 (2003)
11. Halperin, E., Kimmel, G., Sharmir, R.: Tag SNP selection in genotype data for maximizing SNP prediction accuracy. Bioinformatics 21, i195-i203 (2005)
12. Bafna, V., Halldorsson, B.V., Schwartz, R., Clark, A.G., Istrail, S.: Haplotypes and Informative SNP Selection Algorithms: Don't Block Out Information. In: Proceedings of the 7th International Conference on Computational Molecular Biology, pp. 19-26 (2003)
13. Bakker, P.D., Graham, R.R., Altshuler, D., Henderson, B., Haiman, C.: Transferability of tag SNPs to capture common genetic variation in DNA repair genes across multiple population. In: Proceedings of Pacific Symposium on Biocomputing (2006)
14. Halldorsson, B.V., Istrail, S., Vega, F.D.L.: Optimal selection of SNP markers for disease association studies. American Journal of Epidemiology 58(3-4), 190-202 (2004)
15. Lee, P.H.: Computational haplotype analysis: An overview of computational methods in genetic variation study. Technical Report, -512, Queen's University, Kingston, ON, Canada (2006), WEB URL: http://www.cs.queensu.ca/TechReports/ Reports/2006-512.pdf
16. Ramensky, V., Sunyaev, S.: Human non-synonymous SNPs: surver and survey. Nucleic Acid Research 30, 3894-3900 (2002)
17. Ng, P., Henikoff, S.: Predicting deleterious amino acid substitutions. Genome Research 11, 863-874 (2001)
18. Reumers, J., Schymkowitz, J., Ferkinghoff-Borg, J., Stricher, F., Serrano, L., Rousseau, F.: SNPeffect: a database mapping molecular phenotypic effects of human non-synonymous coding SNPs. Nucleic Acid Research 33, D527-532 (2005)
19. Yue, P., Melamud, E., Moult, J.: SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinformatics 7, 166 (2006)
20. Karchin, R., et al.: LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics 21, 2814-2820 (2005)
21. Cartegni, L., Wang, J., Zhu, Z., Zhang, M.Q., Krainer, A.R.: ESEfinder: A web resource to identify exonic splicing enhancers. Nucleic Acids Research 31, 3568-3571 (2003)
22. Yeo, G., Burge, C.B.: Variation in sequence and organization of splicing regulatory elements in vertebrate genes. In the Proceeding of Proc. Natl. Acad. Sci. 101(44), 15700-15705 (2004)
23. Fairbrother, W.G., Yeh, R.F., Sharp, P.A., Burge, C.B.: Predictive identification of exonic splicing enhancers in human genes. Science 297, 1007-1013 (2002)
24. Zhang, et al.: Exon inclusion is dependent on predictable exonic splicing enhancers. Molecular and Cellular Biology 25(16), 7323-7332 (2005)
25. Akiyama, Y.: TFSEARCH: Searching Transcription Factor Binding Sites (1998), WEB URL: http://www.rwcp.or.jp/papia/
26. Sandelin, A., Wasserman, W.W., Lenhard, B.: ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Research 32, W249-252 (2004)
27. Hubbard, T.J.P., et al.: Ensembl, Nucleic Acids Research (Database issue) (2007)
28. Karolchik, D., et al.: The ucsc genome browser database. Nucl. Acids Res. 31(1), 51-54 (2003)
29. Krawczak, M., Thomas, N.S., Hundrieser, B., Mort, M., Wittig, M., Hampe, J., Cooper, D.N.: Single base-pair substitutions in exon-intron junctions of human genes: nature, distribution, and consequences for mrna splicing. Human Mutation 28(2), 150-158 (2007)
30. McKusick-Nathans Institute of Genetic Medicine, J.H.U., National Center for Biotechnology Information, N.L.o.M.: Online Mendelian Inheritance in Man, OMIM (TM). WEB URL: http://www.nebi.nlm.nih.gov/omim/
31. The International HapMap Consortium,: The International HapMap Project. Nature 426, 789-796 (2003)
32. Hedrick, P.: Gametic disequilibrium measures: proceed with caution. Genetics 117, 331-341 (1987)
33. Lee, S.M.: Goal programming for decision analysis. Auerback, Philadelphia (1972)