Allelic drop-out in the LDLR gene affects mutation detection in familial hypercholesterolemia

Allelic dropout in PAH affecting the results of genetic diagnosis in phenylketonuria

OBJECTIVES

Phenylketonuria (PKU) is an inherited autosomal recessive disorder of phenylalanine metabolism. It is mainly caused by a deficiency in phenylalanine hydroxylase (PAH) and frequently diagnosed with Sanger sequencing. To some extent, allelic dropout can explain the inconsistency in genotype and phenotype.

METHODS

Three families were evaluated through DNA sequence analysis, multiplex ligation-dependent probe amplification (MLPA) and prenatal diagnosis technologies. The possibility of inconsistency in phenotype and genotype with c.331C>T variant was analysed.

RESULTS

Through pedigree analysis, three mothers carried a homozygous c.331C>T variant, which was a false-positive result. New primers were used, and this error was caused by allelic dropout. In this case, c.158G>A was likely a benign variant.

CONCLUSIONS

Sequence variants in primer-binding regions could cause allelic dropout, creating unpredictable errors in genotyping. Our results emphasised the need for careful measures to treat genotype-phenotype inconsistencies.

Molecular testing of 163 patients with Morquio A (Mucopolysaccharidosis IVA) identifies 39 novel GALNS mutations

Morquio A (Mucopolysaccharidosis IVA; MPS IVA) is an autosomal recessive lysosomal storage disorder caused by partial or total deficiency of the enzyme galactosamine-6-sulfate sulfatase (GALNS; also known as N-acetylgalactosamine-6-sulfate sulfatase) encoded by the GALNS gene. Patients who inherit two mutated GALNS gene alleles have a decreased ability to degrade the glycosaminoglycans (GAGs) keratan sulfate and chondroitin 6-sulfate, thereby causing GAG accumulation within lysosomes and consequently pleiotropic disease. GALNS mutations occur throughout the gene and many mutations are identified only in single patients or families, causing difficulties both in mutation detection and interpretation. In this study, molecular analysis of 163 patients with Morquio A identified 99 unique mutations in the GALNS gene believed to negatively impact GALNS protein function, of which 39 are previously unpublished, together with 26 single-nucleotide polymorphisms. Recommendations for the molecular testing of patients, clear reporting of sequence findings, and interpretation of sequencing data are provided.

Allele dropout caused by a non-primer-site SNV affecting PCR amplification--a call for next-generation primer design algorithm

BACKGROUND

PCR-based technology is indispensable for genetic diagnosis. On the other hand, allele dropout is one significant cause of genotyping errors. Most allele dropout mechanisms are related to annealing failure caused by single nucleotide variant (SNV) situated inside the primer sequences. Here, we demonstrate a novel allele dropout mechanism caused by a non-primer-binding-site SNV.

METHODS

We demonstrate that the apparent homozygosity of NM_000137.1(FAH):c.1035_1037del was caused by allele dropout.

RESULTS

The non-primer-binding-site SNV causes a strong secondary hairpin structure formation of the PCR products and leads to amplification failure. SNV check of the primer sequences per se during primer design is not adequate to avoid allele dropout.

CONCLUSIONS

The next-generation primer design software should analyze the secondary structure of primers and template sequence taking SNV in both sequences into account in order to avoid genotyping errors.

Identification of gene mutations in autosomal dominant polycystic kidney disease through targeted resequencing

Mutations in two large multi-exon genes, PKD1 and PKD2, cause autosomal dominant polycystic kidney disease (ADPKD). The duplication of PKD1 exons 1-32 as six pseudogenes on chromosome 16, the high level of allelic heterogeneity, and the cost of Sanger sequencing complicate mutation analysis, which can aid diagnostics of ADPKD. We developed and validated a strategy to analyze both the PKD1 and PKD2 genes using next-generation sequencing by pooling long-range PCR amplicons and multiplexing bar-coded libraries. We used this approach to characterize a cohort of 230 patients with ADPKD. This process detected definitely and likely pathogenic variants in 115 (63%) of 183 patients with typical ADPKD. In addition, we identified atypical mutations, a gene conversion, and one missed mutation resulting from allele dropout, and we characterized the pattern of deep intronic variation for both genes. In summary, this strategy involving next-generation sequencing is a model for future genetic characterization of large ADPKD populations.

Combining multiple PCR primer pairs for each amplicon can improve SNP genotyping accuracy by reducing allelic drop-out

We have developed a systematic, single-tube assay approach to reduce the chance of SNP genotyping error due to otherwise unidentifiable allelic drop-out during PCR amplification. Allelic drop-out in such cases would normally be caused by additional and rare genetic variation within the PCR primer site sequence itself. Our method is novel in that it does not require prior knowledge of the additional "hidden" genetic variation. The method has been tested in multiplex using a microarray-based SNP genotyping chip and results in the rescue of previously reported false genotype calls.

Preimplantation genetic diagnosis for beta-thalassemia using single-cell DNA analysis for codons 17 and 26 of beta-globin gene

BACKGROUND

Preimplantation genetic diagnosis (PGD) of monogenic autosomal hereditary disorders following assisted conception usually involves the removal of one or two blastomeres from preimplantation embryos. However, the amount of DNA from a single blastomere is insufficient to amplify the region of interest. Hence, the whole genome amplification (WGA) method is performed prior to amplifying the genes of interest before analysis of DNA material through polymerase chain reaction (PCR).

METHODS

In the present study we report that WGA from a single blastomere extracted from unwanted preimplantation human embryos (obtained from 10 infertile couples) could positively yield microgram quantities of amplified DNA allowing PCR analysis for codons 17 and 26 of the beta-globin gene that cause the beta-thalassemia disorder. We developed a rapid and highly specific technique of single-cell PCR to amplify a specific region on the beta-globin gene for codon 17 (AAG-->TAG) and codon 26 (GAG-->AAG) by using single-cell PCR.

RESULTS

About 249 bp of amplicon for codon 17 and about 200 bp of amplicon for codon 26 were successfully amplified. No mutations were observed. Analyzed embryos were not transferred back to patients because the embryos used as samples were wasted embryos.

CONCLUSIONS

Compared to other approaches for prenatal diagnosis, PGD is rapid and suitable as a noninvasive clinical tool for identifying genetic disorders for the purpose of reducing selective miscarriages and moral dilemmas. We opine that DNA extraction and amplification can be successfully performed by using single-cell PCR to diagnose genetic diseases before pregnancy.

Development of a universal chemiluminometric genotyping method for high-throughput detection of 7 LDLR gene mutations in Greek population

OBJECTIVES

Familial hypercholesterolemia (FH) is caused by mutations in the LDL receptor (LDLR) gene. We report the application of a universal method with high allele discrimination properties to the simultaneous genotyping of 7 LDLR mutations in Greeks, in dry-reagent format.

DESIGN AND METHODS

We genotyped mutations C858A, C939A, G1285A, T1352C, G1646A, G1775A, C/T81G. Unpurified amplicons from a multiplex PCR that produced fragments encompassing all 7 mutations were subjected to probe extension reactions in the presence of fluorescein-modified dCTP, and a microtiter well-based assay of extension products with a peroxidase-antifluorescein conjugate and a chemiluminogenic substrate. We used lyophilized dry reagents and assigned genotypes by the signal ratio of normal-to-mutant-specific probe.

RESULTS

We standardized the method and optimised all steps for specificity. The method was validated by genotyping blindly 119 (833 genotypings). Results were fully concordant with other methods used as standards.

CONCLUSIONS

This method is accurate, simple, rapid and robust. The microtiter well format allows genotyping of a large number of samples in parallel for several mutations.