Frequency of common HFE variants in the Saudi population: a high throughput molecular beacon-based study

Abstract

Background: Hereditary Hemochromatosis (HH) is an autosomal recessive disorder highlighted by iron-overload. Two popular mutations in HFE, p.C282Y and p.H63D, have been discovered and found to associate with HH in different ethnic backgrounds. p.C282Y and p.H63D diagnosis is usually made by restriction enzyme analysis. However, the use of this technique is largely limited to research laboratories because they are relatively expensive, time-consuming, and difficult to transform into a high throughput format.

Methods: Single nucleotide variations in target DNA sequences can be readily identified using molecular beacon fluorescent probes. These are quenched probes with loop and hairpin structure, and they become fluorescent upon specific target recognition. We developed high throughput homogeneous real-time PCR assays using molecular beacon technology, to genotype p.C282Y and p.H63D variants. Representative samples of different genotypes for these variants were assayed by restriction enzyme analysis and direct sequencing as bench mark methods for comparison with the newly developed molecular beacon-based real-time PCR assay.

Results: Complete concordance was achieved by all three assay formats. Homozygotes (mutant and wildtype) and heterozygotes were readily differentiated by the allele specific molecular beacons as reported by the associated fluorophore in the real-time assay developed in this study. Additionally, these assays were used in a high throughput format to establish the allele frequency of C282Y and H63D in Saudis for the first time.

Conclusion: These assays may be reliably applied as a diagnostic test or large scale method for population screening.

Figure 1

2% agarose gel showing the restriction digestion fragments for detection of p.C282Y (1A) and p.H63D (1B) mutations. Undigested (UD), normal (+/+), mutant (-/-), and heterozygote (+/-).

Figure 2

FAM signal; TET signal Representative real-time PCR genotyping results for p.C282Y variants are shown. (A) Normal (FAM positive, TET negative), (B) mutant genotype (FAM negative TET positive), and (C) heterozygote (FAM positive TET positive).

Figure 3

FAM signal; TET signal Representative real-time PCR genotyping results for p.C282Y variants are shown. (A) Normal (FAM positive, TET negative), (B) mutant genotype (FAM negative TET positive), and (C) heterozygote (FAM positive TET positive).