Artif Intell Med - Multi-marker tagging single nucleotide polymorphism selection using estimation of distribution algorithms.

Tópicos

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Resumo

JECTIVES: This paper presents an optimization algorithm for the automatic selection of a minimal subset of tagging single nucleotide polymorphisms (SNPs).METHODS AND MATERIALS: The determination of the set of minimal tagging SNPs is approached as an optimization problem in which each tagged SNP can be covered by a single tagging SNP or by a pair of tagging SNPs. The problem is solved using an estimation of distribution algorithm (EDA) which takes advantage of the underlying topological structure defined by the SNP correlations to model the problem interactions. The EDA stochastically searches the constrained space of feasible solutions. It is evaluated across HapMap reference panel data sets.RESULTS: The EDA was compared with a SAT solver, able to find the single-marker minimal tagging sets, and with the Tagger program. The percentage of reduction ranged from 10% to 43% in the number of tagging SNPs of the minimal multi-marker tagging set found by the EDA with respect to the other algorithms.CONCLUSIONS: The introduced algorithm is effective for the identification of minimal multi-marker SNP sets, which considerably reduce the dimension of the tagging SNP set in comparison with single-marker sets. Other variants of the SNP problem can be treated following the same approach.

Resumo Limpo

jectiv paper present optim algorithm automat select minim subset tag singl nucleotid polymorph snpsmethod materi determin set minim tag snps approach optim problem tag snp can cover singl tag snp pair tag snps problem solv use estim distribut algorithm eda take advantag under topolog structur defin snp correl model problem interact eda stochast search constrain space feasibl solut evalu across hapmap refer panel data setsresult eda compar sat solver abl find singlemark minim tag set tagger program percentag reduct rang number tag snps minim multimark tag set found eda respect algorithmsconclus introduc algorithm effect identif minim multimark snp set consider reduc dimens tag snp set comparison singlemark set variant snp problem can treat follow approach

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