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A network algorithm for the X chromosomal exact test for Hardy–Weinberg equilibrium with multiple alleles

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10.1111/1755-0998.13373
 
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Graffelman, JanMés informacióMés informacióMés informació
Ortoleva, Leonardo
Document typeArticle
Defense date2021-07-01
Rights accessOpen Access
All rights reserved. This work is protected by the corresponding intellectual and industrial property rights. Without prejudice to any existing legal exemptions, reproduction, distribution, public communication or transformation of this work are prohibited without permission of the copyright holder
ProjectTRANSFERENCIA Y DESARROLLO METODOLOGICO DE TECNICAS COMPOSICIONALES PARA LAS CIENCIAS APLICADAS Y LA INGENIERIA (AEI-RTI2018-095518-B-C22)
Abstract
Statistical methodology for testing the Hardy-Weinberg equilibrium at X chromosomal variants has recently experienced considerable development. Up to a few years ago, testing X chromosomal variants for equilibrium was basically done by applying autosomal test procedures to females only. At present, male alleles can be taken into account in asymptotic and exact test procedures for both the bi-and multiallelic case. However, current X chromosomal exact procedures for multiple alleles rely on a classical full enumeration algorithm and are computationally expensive, and in practice not feasible for more than three alleles. In this article, we extend the autosomal network algorithm for exact Hardy-Weinberg testing with multiple alleles to the X chromosome, achieving considerable reduction in computation times for multiallelic variants with up to five alleles. The performance of the X chromosomal network algorithm is assessed in a simulation study. Beyond four alleles, a permutation test is, in general, the more feasible approach. A detailed description of the algorithm is given, and examples of X chromosomal indels and microsatellites are discussed.
CitationGraffelman, J.; Ortoleva, L. A network algorithm for the X chromosomal exact test for Hardy–Weinberg equilibrium with multiple alleles. "Molecular ecology resources", July 2021, vol. 21, núm. 5, p. 1547-1557. 
URIhttp://hdl.handle.net/2117/343817
DOI10.1111/1755-0998.13373
ISSN1755-098X
Publisher versionhttps://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13373
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