The number of markers in the HapMap project: some notes on chi-square and exact tests for Hardy-Weinberg equilibrium

FCER2 T2206C variant associated with FENO levels in asthmatic children using inhaled corticosteroids: The PACMAN study

BACKGROUND

The FCER2 gene, via encoding of the CD23 receptor, plays an important role in the regulation of IgE responses. A genetic variant of the FCER2 gene (T2206C) was previously shown to be associated with IgE levels in asthmatic children. IgE sensitization has also been linked to increased levels of fractional exhaled nitric oxide (FENO).

OBJECTIVE

To investigate whether the FCER2 T2206C variant influences FENO levels in asthmatic children with a reported use of inhaled corticosteroids (ICS).

METHODS

This cross-sectional study involved 593 asthmatic children with a reported use of ICS, availability of FENO measurements and genotyping data on the FCER2 T2206C variant (rs28364072). An additive genetic model was assumed, and the association between the FCER2 T2206C variant and the log-transformed (ln) FENO levels was evaluated using linear regression analysis, adjusted for age, sex, adapted British Thoracic Society (BTS) treatment steps and atopy.

RESULTS

The mean age of the population was 9.1 ± 2.2 years, and the median of FENO levels was 13.0 ppb with an interquartile range (IQR) of (8.0-27.5 ppb). The minor allele (G) frequency of rs28364072 was 29.6%, and each extra copy of the G allele was significantly associated with a lower level of the geometric mean of FENO (log scale, β = -0.12, 95% CI: -0.23, -0.02).

CONCLUSION AND CLINICAL RELEVANCE

Our results showed that the FCER2 T2206C variant was significantly associated with lower FENO levels in carriers of the G allele. Nevertheless, this SNP contributed little to the variability in FENO levels in this patient population. Our findings contribute to the present knowledge on FENO in asthmatic children; however, future replication studies are required to establish the role of this gene in relation to FENO.

Benzimidazole resistance in Haemonchus contortus recovered from farmed red deer

Thirty Haemonchus contortus male worms were collected from farmed red deer yearlings in order to determine whether routine administration of albendazole for a long-term period (17 years) could select anthelmintic resistance. PCR-RFLP method based on single-nucleotide polymorphism of codon 200 in isotype 1 ß-tubulin gene (Phe200Tyr) was applied. The results showed a significant frequency of either the resistant allele (85 %) or the homozygous resistant genotype (70 %). By chi-square test, Hardy-Weinberg equilibrium of the population was accepted (p = 0.334, power of test 0.01). True prevalence of the resistant genotype (RR) was estimated to be 46.5-87.2 % (confidence interval 95 %) calculated by Sterne's exact method. These results confirmed that long-term use of benzimidazoles could change the relative allele frequency of genes associated with drug resistance and may cause a large-scale spread of the resistant allele. To our knowledge, this study supported benzimidazole resistance in Haemonchus contortus in red deer for the first time.

Detecting false-positive signals in exome sequencing

Disease gene discovery has been transformed by affordable sequencing of exomes and genomes. Identification of disease-causing mutations requires sifting through a large number of sequence variants. A subset of the variants are unlikely to be good candidates for disease causation based on one or more of the following criteria: (1) being located in genomic regions known to be highly polymorphic, (2) having characteristics suggesting assembly misalignment, and/or (3) being labeled as variants based on misleading reference genome information. We analyzed exome sequence data from 118 individuals in 29 families seen in the NIH Undiagnosed Diseases Program (UDP) to create lists of variants and genes with these characteristics. Specifically, we identified several groups of genes that are candidates for provisional exclusion during exome analysis: 23,389 positions with excess heterozygosity suggestive of alignment errors and 1,009 positions in which the hg18 human genome reference sequence appeared to contain a minor allele. Exclusion of such variants, which we provide in supplemental lists, will likely enhance identification of disease-causing mutations using exome sequence data.

Approximate and exact tests of Hardy-Weinberg equilibrium using uncertain genotypes

Testing for Hardy-Weinberg equilibrium (HWE) is commonly used as a quality control filter in genome-wide scans for markers with experimentally determined genotypes. In contrast, for markers with imputed genotypes, there are post-imputation metrics of quality that can be used as screens but there are no formal tests of deviation from HWE. Similarly, there are no formal tests of deviation from HWE for probabilistic genotypes that are generated by sequencing projects. Here, I describe generalizations of the approximate χ(2) and exact tests of HWE for use with uncertain genotypes. The tests fully account for the probabilities of all possible genotypes at a marker for each individual. By computer simulation, the approximate and exact tests are shown to maintain valid control of the type I error rate. Calculations of the loss of power as the uncertainty in genotypes increases are illustrated. The tests are compatible with chip-based genotypes for single-nucleotide polymorphisms and copy number polymorphisms, imputed genotypes, and probabilistic assignments of genotype from variable-coverage sequence data.