Data from: Multi-allelic exact tests for Hardy-Weinberg equilibrium that account for gender

Statistical tests for Hardy-Weinberg equilibrium are important elementary tools in genetic data analysis. X-chromosomal variants have long been tested by applying autosomal test procedures to females only, and gender is usually not considered when testing autosomal variants for equilibrium. Recently, we proposed specific X-chromosomal exact test procedures for bi-allelic variants that include the hemizygous males, as well as autosomal tests that consider gender. In this paper we present the extension of the previous work for variants with multiple alleles. A full enumeration algorithm is used for the exact calculations of triallelic variants. For variants with many alternate alleles we use a permutation test. Some empirical examples with data from the 1000 genomes project are discussed.

哈迪-温伯格平衡（Hardy-Weinberg equilibrium）统计检验是遗传数据分析中重要的基础工具。长期以来，X染色体变异体的检验仅通过将常染色体检验流程应用于女性样本开展，且在检验常染色体变异体的平衡时通常不会考虑性别因素。近期，我们针对包含半合子男性的双等位基因变异体提出了专属的X染色体精确检验流程，同时也提出了考虑性别因素的常染色体检验方法。本文针对多等位基因变异体拓展了前述研究工作。针对三等位基因变异体的精确计算，我们采用全枚举算法；对于拥有大量替代等位基因的变异体，我们采用置换检验。本文还讨论了基于千人基因组计划（1000 Genomes Project）数据的若干实证案例。