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.

用于哈迪-温伯格平衡（Hardy-Weinberg equilibrium）的统计检验，是遗传数据分析领域重要的基础性工具。长期以来，X染色体变异的检验仅针对女性群体套用常染色体检验流程，而在检验常染色体变异的平衡状态时，通常不会考虑性别因素。近期，我们针对纳入半合子男性样本的双等位基因变异，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拓展了此前的研究工作：对于三等位基因变异，采用全枚举算法完成精确计算；对于携带大量变异等位基因的变异，则使用置换检验（permutation test）。此外，本文还讨论了若干基于千人基因组计划（1000 Genomes Project）实测数据的实证案例。