Simulation of Y-chromosomal haplotype data
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Date
2010
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Publisher
Elsevier
Abstract
The non-recombining nature of the Y-chromosome determines the non-independence of alleles between
loci. The evolution of short tandem repeat (STR) loci in the Y-chromosome is the result of different factors
such as differential mutation rates, mutation modes, gene conversion, selection and demographic processes.
The degree of correlation between loci is dependent on the magnitude of these processes. The simulation
of data is a routine tool used for testing hypotheses in population and evolutionary studies. The
most basic parameters hitherto used in lineage haplotype simulations are the allele frequency distributions
and mutation rates, assuming either full independence or linkage between loci. In this study we
introduce use of the Spearman correlation coefficient to estimate the degree of dependence between
non-recombining loci. Then, both the interdependence between loci and the allele frequency distributions
at multi-allelic loci are incorporated in an algorithm for simulating haplotypes. We illustrate the
method using published and unpublished Y-chromosome STR data.
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Keywords
Haplotype simulation, Inter-locus correlation, Y-chromosome
Citation
Koen, C. & D’Amato, M.E. (2010). Simulation of Y-chromosomal haplotype data. Mathematical Biosciences, 224: 24-28