Information Technologies in Biomedicine pp 357-364 | Cite as
Application to Estimate Haplotypes for Multiallelic Present-Absent Loci
Conference paper
Summary
The article presents an algorithm and an application to estimate haplotype frequencies from genotype data for unrelated individuals. Presented approach can handle loci with multiple alleles as well as silent (null) alleles. The mathematical model and an expanded Expectation-Maximization algorithm is described. The computer program, called NullHap, available freely at http://staff.elka.pw.edu.pl/ rnowak2/nullhap implements presented ideas. Comparison with known software to estimate haplotypes: Arlequin, PHASE and Haplo-IHP proves the advantage presented method.
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References
- 1.Boettcher, P., Pagnacco, G., Stella, A.: A Monte Carlo Approach for Estimation of Haplotype Probabilities in Half-Sib Families. J. Dairy Sci. 87, 4303–4310 (2004)CrossRefGoogle Scholar
- 2.Botstein, D., Risch, N.: Discovering genotypes underlying human phenotypes: past successes for Mendelian disease, future approaches for complex disease. Nat.Genet. 33, 228–237 (2003)CrossRefGoogle Scholar
- 3.Dempster, A., Laird, N., Rubin, D.: Maximum likelihood from incomplete data via the em algorithm. Journal of the Royal Statistical Society 39, 1–39 (1977)MATHMathSciNetGoogle Scholar
- 4.Douglas, J., et al.: Experimentally derived haplotypes substantially increase the efficiency of linkage disequilibrium studies. Nat. Genet. 28, 361–364 (2001)CrossRefGoogle Scholar
- 5.Excoffier, L., Laval, G., Schneider, S.: Arlequin ver. 3.0: An integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1, 47–50 (2005)Google Scholar
- 6.Excoffier, L.M., Slatkin, M.: Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol. Biol. Evol. 12, 921–927 (1995)Google Scholar
- 7.Morris, R., Kaplan, N.: On the advantage of haplotype analysis in the presence of multiple disease susceptibility alleles. Gen. Epidem. 23, 221–233 (2002)CrossRefGoogle Scholar
- 8.Niu, T., Qin, Z., Xu, X., Liu, J.: Bayesian haplotype inference for multiple linked single nucleotide polymorphisms. Am. J. Hum. Genet. 70, 157–169 (2002)CrossRefGoogle Scholar
- 9.Stephens, M., Smith, N., Donnelly, P.: A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet. 68, 978–989 (2001)CrossRefGoogle Scholar
- 10.Yoo, Y., Tang, J., Kaslow, R., Zhang, K.: Haplotype inference for present-absent genotype data using previously identified haplotypes and haplotype patterns. Bioinformatics 23, 2399–2406 (2007)CrossRefGoogle Scholar
- 11.
- 12.The faif library, http://faif.sourceforge.net/
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© Springer-Verlag Berlin Heidelberg 2008