Simulation of Y-chromosomal haplotype data

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Date

2010

Journal Title

Journal ISSN

Volume Title

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 We illustrate the method using published and unpublished Y-chromosome STR data.

Description

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