descriptionPublicationkeyboard_double_arrow_right Article , Other literature type 20 Sep 2020Publisher:Cold Spring Harbor LaboratoryJournal:Molecular Ecology Resources, volume 21, pages 1,547-1,557 (issn: 1755-098X, eissn: 1755-0998,

Authors: Leonardo Ortoleva; Leonardo Ortoleva; Jan Graffelman; Jan Graffelman;

doi: 10.1101/2020.09.20.305102 , 10.22541/au.160103348.87979451 , 10.1111/1755-0998.13373

pmid: 33687797

pmc: PMC8251783

handle: 2117/343817

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

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Abstract

AbstractStatistical methodology for testing 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.

Related Organizations

UNIVERSITY OF WASHINGTON
Universitat Polite`cnica de Catalunya
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Keywords

Male, Biomatemàtica, :Matemàtiques i estadística::Matemàtica aplicada a les ciències [Àrees temàtiques de la UPC], Classificació AMS::92 Biology and other natural sciences::92B Mathematical biology in general, Numerical analysis--Simulation methods, Hardy-Weinberg equilibrium, :Matemàtiques i estadística::Anàlisi numèrica [Àrees temàtiques de la UPC], X chromosome, Gene Frequency, Network algorithm, Humans, Permutation test, :65 Numerical analysis::65C Probabilistic methods, simulation and stochastic differential equations [Classificació AMS], Indel, Alleles, Biomathematics, Anàlisi numèrica, Chromosomes, Human, X, Models, Genetic, Àrees temàtiques de la UPC::Matemàtiques i estadística::Anàlisi numèrica, RESOURCE ARTICLES, :92 Biology and other natural sciences::92B Mathematical biology in general [Classificació AMS], Microsatellite, simulation and stochastic differential equations, Classificació AMS::65 Numerical analysis::65C Probabilistic methods, simulation and stochastic differential equations, Àrees temàtiques de la UPC::Matemàtiques i estadística::Matemàtica aplicada a les ciències, Classificació AMS::65 Numerical analysis::65C Probabilistic methods, Female, Algorithms

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