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HaploRec: efficient and accurate large-scale reconstruction of haplotypes

DOI: 10.1186/1471-2105-7-542

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Abstract:

We define three novel statistical models and give an efficient algorithm for haplotype reconstruction, jointly called HaploRec. HaploRec is based on exploiting local regularities conserved in haplotypes: it reconstructs haplotypes so that they have maximal local coherence. This approach – not assuming statistical dependence for remotely located markers – has two useful properties: it is well-suited for sparse marker maps, such as those used in gene mapping, and it can actually take advantage of long maps.Our experimental results with simulated and real data show that HaploRec is a powerful method for the large scale haplotyping needed in association studies. With sample sizes large enough for gene mapping it appeared to be the best compared to all other tested methods (Phase, fastPhase, PL-EM, Snphap, Gerbil; simulated data), with small samples it was competitive with the best available methods (real data). HaploRec is several orders of magnitude faster than Phase and comparable to the other methods; the running times are roughly linear in the number of subjects and the number of markers. HaploRec is publicly available at http://www.cs.helsinki.fi/group/genetics/haplotyping.html webcite.The problem we consider is haplotype reconstruction: given the genotypes of a sample of individuals, the task is to predict the most likely haplotype pair for each individual. Computational haplotype reconstruction methods are based on statistical dependency between closely located markers, known as linkage disequilibrium. Many computational methods have been developed for the reconstruction of haplotypes. Some of these methods do not rely on the statistical modeling of the haplotypes [1-3], but most of them, like our proposed algorithm HaploRec, do [4-10]. For a review of these and other haplotyping methods we refer to [11-13]. Laboratory techniques are being developed for direct molecular haplotyping (see, e.g., [14,15]), but these techniques are not mature yet, and are currently t

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