Hardy-Weinberg Equilibrium in the Large Scale Genomic Sequencing Era

Abstract

Hardy-Weinberg Equilibrium (HWE) is used to estimate the number of homozygous and heterozygous variant carriers based on its allele frequency in populations that are not evolving. Deviations from HWE in large population databases have been used to detect genotyping errors, which can result in extreme heterozygote excess (HetExc). However, HetExc might also be a sign of natural selection since recessive disease causing variants should occur less frequently in a homozygous state in the population, but may reach high allele frequency in a heterozygous state, especially if they are advantageous. We developed a filtering strategy to detect these variants and applied it on genome data from 137,842 individuals. The main limitations of this approach were quality of genotype calls and insufficient population sizes, whereas population structure and inbreeding can reduce sensitivity, but not precision, in certain populations. Nevertheless, we identified 161 HetExc variants in 149 genes, most of which were specific to African/African American populations (∼79.5%). Although the majority of them were not associated with known diseases, or were classified as clinically "benign," they were enriched in genes associated with autosomal recessive diseases. The resulting dataset also contained two known recessive disease causing variants with evidence of heterozygote advantage in the sickle-cell anemia (HBB) and cystic fibrosis (CFTR). Finally, we provide supporting in silico evidence of a novel heterozygote advantageous variant in the chromodomain helicase DNA binding protein 6 gene (CHD6; involved in influenza virus replication). We anticipate that our approach will aid the detection of rare recessive disease causing variants in the future.

Keywords: Hardy-Weinberg Equilibrium; association studies in genetics; gnomAD; heterozygote advantage; recessive inheritance.

FIGURE 1

Deviations from Hardy-Weinberg Equilibrium (HWE) in 7 ethnic gnomAD populations. Number of (A) individuals and (B) variants in each population. (C) Minimum variant Allele Frequency (AF) required for statistically significant heterozygote excess according to HWE, in the absence of homozygous individuals in each population. Percentage of variants (raw numbers are shown in B) deviating from HWE due to (D) heterozygote deficiency or (E) heterozygote excess in each population.

FIGURE 2

Comparison of observed ratio between variant Alllele Frequency (AF) and homozygous AF with expected ratio according to Hardy-Weinberg Equilibrium (HWE) in 7 ethnic gnomAD populations: Non-Finnish European (A, NFE), Latino/Admixed American (B, AMR), South Asian (C, SAS), Finnish (D, FIN), African/African American (E, AFR), East Asian (F, EAS), and Ashkenazi Jewish (G, ASJ). Black line represents expected ratio between AF and expected homozygous AF according to HWE. Variants where deviation from HWE are not significant (P > 0.05) are shown in gray, whereas those that deviate from HWE due to heterozygote deficiency or excess are shown in orange and blue respectively. Only variants with 0.001 ≤ AF ≤ 0.05 and homozygous AF ≤ 0.005 are shown.

FIGURE 3

Impact of tandem repeats, segmental duplications and allele balance on the probability of variant deviation from Hardy-Weinberg Equilibrium (HWE) due to heterozygote excess (HetExc). (A) Percentage of variants deviating from HWE due to HetExc that are located in tandem repeat, segmental duplication regions or the reference (“Ref,” all other regions) group. (B) Distribution of Allele Balance (AB) between variant carriers in variants from “Ref” group (error bars indicate standard deviation). For each variant these statistics are aggregated into a single metric that represents cumulative percentage of Variant Carriers with Normal (0.4–0.55) Allele Balance (VCNAB, e.g., 20.0% + 23.4% + 23.0% = 66.4%). (C) Distribution of variants with various VCNAB percentages in “Segmental duplication”, “Tandem repeat” and “Ref” groups. (D) Percentage of variants with VCNAB < 50% in the whole “Ref” group and a subset of variants with statistically significant excess of heterozygotes in “Ref” group. ^****Indicates statistical significance of p ≤ 0.0001.

FIGURE 4

Potential recessive disease causing variants identified by deviation from Hardy-Weinberg Equilibrium (HWE) due to excess of heterozygotes (HetExc). (A) Distribution of variants deviating and not deviating from HWE due to excess of heterozygotes (HetExc and HetExc-, respectively) in 7 ethnic gnomAD populations. (B) Proportions of missense, synonymous and other protein coding variants in HetExc and HetExc- datasets. (C) ClinVar status (e.g., pathogenic/benign) of HetExc variants (D) Known disease associated genes with at least one variant in HetExc and HetExc- datasets grouped by inheritance pattern: autosomal dominant (AD), autosomal recessive (AR) or both. ^∗Indicates statistical significance of p ≤ 0.05.