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不可或缺的基础工具。长期以来，X染色体变异（X-chromosomal variants）的检测仅针对女性群体采用常染色体检验流程（autosomal test procedures），而在针对常染色体变异进行平衡检验时，通常不会考量性别因素。近期，我们针对包含半合子男性（hemizygous males）的双等位基因变异（bi-allelic variants）提出了专属的X染色体精确检验流程，同时也推出了兼顾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：针对三等位基因变异（triallelic variants）的精确计算，采用全枚举算法（full enumeration algorithm）；对于携带大量替代等位基因的变异，则采用置换检验（permutation test）方法。此外，本文结合千人基因组计划（1000 Genomes Project）的数据，讨论了若干实证分析案例。