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

Authors :
Universitat Politècnica de Catalunya. Departament d'Estadística i Investigació Operativa
Universitat Politècnica de Catalunya. COSDA-UPC - COmpositional and Spatial Data Analysis
Graffelman, Jan
Ortoleva, Leonardo
Universitat Politècnica de Catalunya. Departament d'Estadística i Investigació Operativa
Universitat Politècnica de Catalunya. COSDA-UPC - COmpositional and Spatial Data Analysis
Graffelman, Jan
Ortoleva, Leonardo
Publication Year :
2021

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.<br />This work was supported by grant RTI2018‐095518‐B‐C22 (MCIU/AEI/FEDER) of the Spanish Ministry of Science, Innovation and Universities and the European Regional Development Fund, and by grant R01 GM075091 from the United States National Institutes of Health. We thank three anonymous reviewers whose comments have helped us to improve the article.<br />Peer Reviewed<br />Postprint (author's final draft)

Details

Database :
OAIster
Notes :
application/pdf, English
Publication Type :
Electronic Resource
Accession number :
edsoai.on1247079737
Document Type :
Electronic Resource