Clinical utility gene card for: Phenylketonuria

Multiplex Snapshot minisequencing for the detection of common PAH gene mutations in Iranian patients with Phenylketonuria

Background

Phenylketonuria is a common inborn defect of amino acid metabolism in the world. This failure is caused by an autosomal recessive insufficiency of the hepatic enzyme hyperphenylalaninemia (PAH), which catalyzes the irreversible hydroxylation of phenylalanine to tyrosine. More than 1,040 different disease-causing mutations have already been identified in the PAH gene. The most prominent complication of Phenylketonuria, if not diagnosed and treated, is severe mental retardation. Hence, early diagnosis and initiation of nutritional therapy are the most significant measures in preventing this mental disorder. Given these data, we developed a simple and rapid molecular test to detect the most frequent PAH mutations.

Methods

Multiplex assay was developed based on the SNaPshot minisequencing approach to simultaneously perform genotyping of the 10 mutations at the PAH gene. We optimized detection of these mutations in one multiplex PCR, followed by 10 single-nucleotide extension reactions. DNA sequencing assay was also used to verify genotyping results obtained by SNaPshot minisequencing.

Result

All 10 genotypes were determined based on the position and the fluorescent color of the peaks in a single electropherogram. Sequencing results of these frequent mutations showed that by using this method, a 100% detection rate could be achieved in the Iranian population.

Conclusion

SNaPshot minisequencing can be useful as a secondary test in neonatal screening for HPA in neonates with a positive screening test, and it is also suitable for carrier screening. The assay can be easily applied for accurate and time- and cost-efficient genotyping of the selected SNPs in various population.

A capillary electrophoresis-based variant hotspot genotyping method for rapid and reliable analysis of the phenylalanine hydroxylase gene in the Chinese Han population

BACKGROUND AND AIMS

Hyperphenylalaninemia (HPA) is a common autosomal recessive disorder of phenylalanine metabolism, mainly caused by the deficiency of phenylalanine hydroxylase gene (PAH). A simple, fast, and accurate assay to achieve early diagnosis for children with HPA is required.

MATERIALS AND METHODS

In the present study, we established a SNaPshot-based assay that allows the simultaneous genotyping of 96 hotspot variants in the PAH gene. First, 18 Chinese HPA patients were analyzed by next generation sequencing (NGS) and SNaPshot in parallel. Then, the SNaPshot assay was performed to analyze the mutational spectrum of the PAH in 4,276 individuals in Eastern China.

RESULTS

A total of 36 variants in the PAH gene were successfully identified by NGS, while the SNaPshot assay identified 34 PAH variants in these patients. Thus, the SNaPshot assay achieved the sensitivity and specificity of 91.6% and 100.0%, respectively. Furthermore, the carrier rate was approximately 1 in 58 (1.73%) in 4,276 individuals, and c.728G > A was the most common variant.

CONCLUSION

In summary, SNaPshot can accurately and rapidly detect PAH gene variants at a comparable performance and lower cost as compared with NGS. Our results suggest that SNaPshot may serve as a promising approach for a routine genetic test in clinical practice.

Admissions and Cost of Hospitalisation of Phenylketonuria: Spanish Claims Database Analysis

BACKGROUND

Phenylketonuria is a well-known rare disease included in the neonatal screening of many countries. Therefore, there are few published data on the admissions and costs of phenylketonuria in Spain.

OBJECTIVE

The objective of this study was to assess the number of admissions and the economic burden of phenylketonuria in Spain.

METHODS

Patients with phenylketonuria were identified from a Spanish database containing data from public and private healthcare centres from 1997 to 2015. The parameters obtained were characteristics of the patients, type of admissions, readmissions, discharges, length of stay, medical service, annual number of visits, annual number of patients, visit-associated costs and patient-associated costs.

RESULTS

Five hundred and ninety-four patients with phenylketonuria were identified: 48.32% were male with a mean (standard deviation) age of 4.50 (10.23) years. The hospital admissions were divided into emergency visits (55.94%) and scheduled visits (43.92%). The majority of patients were discharged home (98.86%). The mean (standard deviation) duration of stay was 4.04 (4.98) days. The number of admissions per year ranged between 13 and 88, with an average of 1.18 admissions per patient per year. Finally, the mean cost per visit increased from €1064.91 to €3709.40, and the mean cost per patient increased from €1818.90 to €4239.32 from 1999 to 2015.

CONCLUSIONS

The access to economic and social data on phenylketonuria in Spain has been updated. The number of admissions in Spain between 1997 and 2015 and healthcare costs between 1999 and 2015 were calculated. There were 24 admissions as a result of a phenylketonuria diagnosis in 2015 and the mean healthcare cost per patient was €4239.32. This information can help to adapt and improve each healthcare system to take into consideration rare diseases.

Molecular Analysis of PKU-Associated PAH Mutations: A Fast and Simple Genotyping Test

Neonatal screening for phenylketonuria (PKU, OMIM: 261600) was introduced at the end of the 1960s. We developed a rapid and simple molecular test for the most frequent phenylalanine hydroxylase (PAH, Gene ID: 5053) mutations. Using this method to detect the 18 most frequent mutations, it is possible to achieve a 75% detection rate in Italian population. The variants selected also reach a high detection rate in other populations, for example, 70% in southern Germany, 68% in western Germany, 76% in Denmark, 68% in Sweden, 63% in Poland, and 60% in Bulgaria. We successfully applied this confirmation test in neonatal screening for hyperphenylalaninemias using dried blood spots and obtained the genotype in approximately 48 h. The method was found to be suitable as second tier test in neonatal screening for hyperphenylalaninemias in neonates with a positive screening test. This test can also be useful for carrier screening because it can bypass the entire coding sequence and intron–exon boundaries sequencing, thereby overcoming the questions that this approach implies, such as new variant interpretations.

Incidence of Neonatal Hyperphenylalaninemia Based on High-performance Liquid Chromatography Confirmatory Technique in Mazandaran Province, Northern Iran (2007-2015)

Background:

Classic phenylketonuria (PKU) is a metabolic disorder. The purpose of this study was to assess epidemiological factors of PKU phenotypes in a neonatal screening program for Mazandaran, Iran.

Methods:

In this descriptive-retrospective study from 2007 to 2015, neonates PKU level was conducted by phenylalanine level based on a biochemical technique by ELISA and then by confirmatory methods high performance liquid chromatography.

Results:

Of the 407,244 screened newborns (48.7% girls and 51.3% boys), 14 girls and 13 boys were diagnosed definitely from 465 suspicious cases of PKU. The incidence of PKU was 0.66 in 10,000, which was noted in different severity (severe PKU - 1:67,874, mild PKU - 1:45,249, and HPA - 1:33,937). In addition, we did not detect any cases of nonclassic PKU.

Conclusions:

Although the consanguineous marriage pattern is a major cause of hyperphenylalaninemia (HPA) particularly in Iranian, there was no significant difference between groups in this study. Now, screening should be executed for all of the family that they have the familial history of PKU in Iran. According to varies actual of prevalence and incidence rate of PKU reported a real patient and taking PKU with mild PKU and HPA, it is recommended, the will provide the PKU reports based on the severity of the disease.

A Novel Variant in the PAH Gene Causing Phenylketonuria in an Iranian Pedigree

BACKGROUND

Phenylalanine hydroxylase (PAH) gene is the well-known causative gene for classic Phenylketonuria (PKU) (OMIM#261600) disease, with more than 500 reported mutations. Through this study, a novel mutation in the PAH gene in an Iranian pedigree with phenylketonuria was introduced.

METHODS

A consanguineous family with a 10-year old affected girl was referred for genetic analysis. Mutation screening of all exons and exon-intron boundaries was performed by Sanger sequencing, and mini haplotype analysis was carried out by genotyping of Short Tandem Repeat (STR) and Variable Number Tandem Repeat (VNTR) alleles.

RESULTS

Mutation analysis revealed a novel homozygous insertion of a single adenine nucleotide at position 335 in exon 3 of the PAH gene. Based on the American College of Medical Genetics and Genomics (ACMG) guidelines, the change is interpreted as a pathogenic mutation which produces a premature termination signal (TAA) at codon 113 according to in silico assessments. The mini haplotype analysis showed that this mutation was linked to STR (15) -VNTR (3).

CONCLUSION

In this study, a novel mutation was reported in a patient who had PKU symptoms without any previously reported mutations in the PAH gene (NM_000277.1:p.Asp112Glufs*2) that can be responsible for the classical PKU phenotype in the Iranian population. Detection of novel mutations indicates notable allelic heterogeneity of the PAH locus among this population.