Departure from Hardy Weinberg Equilibrium and Genotyping Error

Abstract

Objective: Departure from Hardy Weinberg Equilibrium (HWE) may occur due to a variety of causes, including purifying selection, inbreeding, population substructure, copy number variation or genotyping error. We searched for specific characteristics of HWE-departure due to genotyping error. Methods: Genotypes of a random set of genetic variants were obtained from the Exome Aggregation Consortium (ExAC) database. Variants with <80% successful genotypes or with minor allele frequency (MAF) <1% were excluded. HWE-departure (d-HWE) was considered significant at p < 10E-05 and classified as d-HWE with loss of heterozygosity (LoH d-HWE) or d-HWE with excess heterozygosity (gain of heterozygosity: GoH d-HWE). Missing genotypes, variant type (single nucleotide polymorphism (SNP) vs. insertion/deletion); MAF, standard deviation (SD) of MAF across populations (MAF-SD) and copy number variation were evaluated for association with HWE-departure. Results: The study sample comprised 3,204 genotype distributions. HWE-departure was observed in 134 variants: LoH d-HWE in 41 (1.3%), GoH d-HWE in 93 (2.9%) variants. LoH d-HWE was more likely in variants located within deletion polymorphisms (p < 0.001) and in variants with higher MAF-SD (p = 0.0077). GoH d-HWE was associated with low genotyping rate, with variants of insertion/deletion type and with high MAF (all at p < 0.001). In a sub-sample of 2,196 variants with genotyping rate >98%, LoH d-HWE was found in 29 (1.3%) variants, but no GoH d-HWE was detected. The findings of the non-random distribution of HWE-violating SNPs along the chromosome, the association with common deletion polymorphisms and indel-variant type, and the finding of excess heterozygotes in genomic regions that are prone to cross-hybridization were confirmed in a large sample of short variants from the 1,000 Genomes Project. Conclusions: We differentiated between two types of HWE-departure. GoH d-HWE was suggestive for genotyping error. LoH d-HWE, on the contrary, pointed to natural variabilities such as population substructure or common deletion polymorphisms.

Keywords: Hardy Weinberg Equilibrium (HWE); SNP quality control; association studies in genetics; heterozygosity.

Figure 1

Analysis of genotyped short variations in genomic region 17:56,000,000–64,000,000 (A,B) and genomic region 3:65,000,000–65,500,000 (C,D) from the 1000 Genomes Project, European Population. Upper figures (A,C) show log-transformed p-values for departures from HWE. Lower figures (B,D) show ratios of observed and expected (i.e., under Hardy-Weinberg Equilibrium) frequencies of heterozygous genotypes. Dots indicate true SNPs, rectangles symbolize variants of indel type. The bar (seen in C,D) indicates common deletion variant esv2657253, (http://www.ensembl.org/Homo_sapiens/StructuralVariation/Explore?r=3:65202694--65229573;sv,esv2657253;svf,3513219;vdb,variation). The arrow (seen in A,B) points to a region with of a degenerate repeat structure within the 5' end of the LRRC37A2 with strong homology with sequences of the LRRC37A3 gene, resulting in genotyping error.