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  Haplotype reconstruction for diploid populations

Zhang, J., Vingron, M., & Hoehe, M. R. (2005). Haplotype reconstruction for diploid populations. Human Heredity, 59(3), 144-156. doi:10.1159/000085938.

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Genre: Journal Article
Alternative Title : Hum Hered

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Zhang et al. - HumHeredity.pdf (Any fulltext), 260KB
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 Creators:
Zhang, Jian, Author
Vingron, Martin1, Author              
Hoehe, Margret R.2, Author              
Affiliations:
1Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              
2Genetic Variation, Haplotypes, and Genetics of Complex Disease (Margret Hoehe), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479651              

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Free keywords: Haplotype analysis; Haplotype likelihood; Multiple SNPs; Unlinked SNPs; Markov chain Monte Carlo; Empirical Bayes; Evolutionary tree
 Abstract: The inference of haplotype pairs directly from unphased genotype data is a key step in the analysis of genetic variation in relation to disease and pharmacogenetically relevant traits. Most popular methods such as Phase and PL do require either the coalescence assumption or the assumption of linkage between the single-nucleotide polymorphisms (SNPs). We have now developed novel approaches that are independent of these assumptions. First, we introduce a new optimization criterion in combination with a block-wise evolutionary Monte Carlo algorithm. Based on this criterion, the 'haplotype likelihood', we develop two kinds of estimators, the maximum haplotype-likelihood (MHL) estimator and its empirical Bayesian (EB) version. Using both real and simulated data sets, we demonstrate that our proposed estimators allow substantial improvements over both the expectation-maximization (EM) algorithm and Clark's procedure in terms of capacity/scalability and error rate. Thus, hundreds and more ambiguous loci and potentially very large sample sizes can be processed. Moreover, applying our proposed EB estimator can result in significant reductions of error rate in the case of unlinked or only weakly linked SNPs.

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Language(s): eng - English
 Dates: 2005-05-26
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Type: -
 Identifiers: eDoc: 268539
DOI: 10.1159/000085938
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Title: Human Heredity
  Alternative Title : Hum Hered
Source Genre: Journal
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Pages: - Volume / Issue: 59 (3) Sequence Number: - Start / End Page: 144 - 156 Identifier: ISSN: 0001-5652