Efficient Genotype Elimination via Adaptive Allele Consolidation

N. De Francesco; G. Lettieri; L. Martini

doi:10.1109/TCBB.2012.46

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2012
Issue No. 4 - July-Aug.
Abstract - Efficient Genotype Elimination via Adaptive Allele Consolidation

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Efficient Genotype Elimination via Adaptive Allele Consolidation

July-Aug. 2012 (vol. 9 no. 4)

pp. 1180-1189

	ASCII Text	x
	N. De Francesco, G. Lettieri, L. Martini, "Efficient Genotype Elimination via Adaptive Allele Consolidation," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 4, pp. 1180-1189, July-Aug., 2012.

	BibTex	x
	@article{ 10.1109/TCBB.2012.46, author = {N. De Francesco and G. Lettieri and L. Martini}, title = {Efficient Genotype Elimination via Adaptive Allele Consolidation}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {9}, number = {4}, issn = {1545-5963}, year = {2012}, pages = {1180-1189}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2012.46}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }

	RefWorks Procite/RefMan/Endnote	x
	TY - JOUR JO - IEEE/ACM Transactions on Computational Biology and Bioinformatics TI - Efficient Genotype Elimination via Adaptive Allele Consolidation IS - 4 SN - 1545-5963 SP1180 EP1189 EPD - 1180-1189 A1 - N. De Francesco, A1 - G. Lettieri, A1 - L. Martini, PY - 2012 KW - molecular biophysics KW - bioinformatics KW - cellular biophysics KW - combinatorial mathematics KW - genetics KW - Celer tool KW - genotype elimination KW - adaptive allele consolidation KW - Lange-Goradia algorithm KW - pedigrees KW - Mendelian inheritance law KW - genetic data error KW - linkage analysis KW - haplotype imputation KW - combinatorial problem KW - Vectors KW - Heuristic algorithms KW - Genetics KW - Bioinformatics KW - Computational biology KW - Polynomials KW - Couplings KW - pedigree. KW - Genotype elimination KW - allele consolidation VL - 9 JA - IEEE/ACM Transactions on Computational Biology and Bioinformatics ER -

N. De Francesco, Dipt. di Ing. dell'Inf.: Elettron., Inf., Telecomun, Univ. di Pisa, Pisa, Italy

G. Lettieri, Dipt. di Ing. dell'Inf.: Elettron., Inf., Telecomun., Univ. di Pisa, Pisa, Italy

L. Martini, S.p.A., Pisa, Italy

DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2012.46

We propose the technique of Adaptive Allele Consolidation, that greatly improves the performance of the Lange-Goradia algorithm for genotype elimination in pedigrees, while still producing equivalent output. Genotype elimination consists in removing from a pedigree those genotypes that are impossible according to the Mendelian law of inheritance. This is used to find errors in genetic data and is useful as a preprocessing step in other analyses (such as linkage analysis or haplotype imputation). The problem of genotype elimination is intrinsically combinatorial, and Allele Consolidation is an existing technique where several alleles are replaced by a single "lumped” allele in order to reduce the number of combinations of genotypes that have to be considered, possibly at the expense of precision. In existing Allele Consolidation techniques, alleles are lumped once and for all before performing genotype elimination. The idea of Adaptive Allele Consolidation is to dynamically change the set of alleles that are lumped together during the execution of the Lange-Goradia algorithm, so that both high performance and precision are achieved. We have implemented the technique in a tool called Celer and evaluated it on a large set of scenarios, with good results.

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Index Terms:

molecular biophysics,bioinformatics,cellular biophysics,combinatorial mathematics,genetics,Celer tool,genotype elimination,adaptive allele consolidation,Lange-Goradia algorithm,pedigrees,Mendelian inheritance law,genetic data error,linkage analysis,haplotype imputation,combinatorial problem,Vectors,Heuristic algorithms,Genetics,Bioinformatics,Computational biology,Polynomials,Couplings,pedigree.,Genotype elimination,allele consolidation

Citation:

N. De Francesco, G. Lettieri, L. Martini, "Efficient Genotype Elimination via Adaptive Allele Consolidation," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 9, no. 4, pp. 1180-1189, July-Aug. 2012, doi:10.1109/TCBB.2012.46

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