Molecular genetics of a cohort of 635 cases of phenylketonuria in a consanguineous population

The investigation of serum phenylalanine levels based on infant feeding method: a cross-sectional study of children less than two years old with phenylketonuria (PKU)

BACKGROUND

Clinical advice may suggest discontinuing breastfeeding after the diagnosis of phenylketonuria in infants as the only effective way to monitor the newborn's intake and accurate measurement of phenylalanine (Phe). This study aims to investigate the prevalence and duration of breastfeeding, as well as its effect on serum Phe levels in infants with phenylketonuria at Education and Therapy Medical Center, Be'sat Hospital, Iran.

METHODS

We conducted a cross-sectional study of 34 children under two years old diagnosed with phenylketonuria between September 2018 and December 2022. Infants were categorized as breastfed and non-breastfed (bottle-fed) based on their feeding method after diagnosis. Data on age at diagnosis, medical records, demographic information, and anthropometric indices were collected, and infants with incomplete data or mixed feeding (formula + breast milk) were excluded from the study.

RESULTS

Of 94 infants managed in our hospital, 34 had complete medical records. Among the all patients 13 (38%) continued to be breastfed combined with phenylalanine-free amino acid-based protein substitute, while 21 (62%) were did not receive breast milk. The mean duration of breastfeeding was 2.57 ± 0.59 (1-3) months. The mean age at diagnosis was 22.6 ± 18.4 days. Phenylalanine concentrations at diagnosis were mean 10, SD 5.44; range 4-24 mg/dL [0.22-1.33 μmol/L] in the breastfed group and mean 14.3, SD 10.2; range 5-37 mg/dL [0.27-2.05 μmol/L] in the non-breastfed group.Non-breastfed infants had lower serum Phe levels than breastfed infants: mean 3.76, SD 2.10; range 1-7 mg/dL [0.05-0.38 μmol/L] and mean 4.89, SD 3.68; range 2-19 mg/dL [0.11-1.05 μmol/L], respectively, although not statistically significant [(t (34) = 118.0, P = 0.51]. Also we found no significant associations in body measurements for weight, height, and head circumference at birth and final assessment.

CONCLUSIONS

In conclusion, during treatment, there were no statistically significant associations between breastfeeding and serum Phe levels with growth in children with phenylketonuria.

Mutational landscape of phenylketonuria in Iran

To date more than 1000 different variants in the PAH gene have been identified in patients with phenylketonuria (PKU). In Iran, several studies have been performed to investigate the genetics bases of the PKU in different parts of the country. In this study, we have analysed and present an update of the mutational landscape of the PAH gene as well as the population genetics and frequencies of detected variants for each cohort. Published articles on PKU mutations in Iran were identified through a comprehensive PubMed, Google Scholar, Web of Science (ISI), SCOPUS, Elsevier, Wiley Online Library and SID literature search using the terms: "phenylketonuria", "hyperphenylalaninemia", and "PKU" in combination with "Iran", "Iranian population", "mutation analysis", and "Molecular genetics". Among the literature-related to genetics of PKU, 18 studies were on the PKU mutations. According to these studies, in different populations of Iran 1497 patients were included for mutation detection that resulted in detection of 129 different mutations. Results of genetic analysis of the different cohorts of Iranian PKU patients show that the most prevalent mutation in Iran is the pathogenic splice variant c.1066-11G > A, occurring in 19.54% of alleles in the cohort. Four other common mutations were p.Arg261Gln, p.Pro281Leu, c.168 + 5G > C and p.Arg243Ter (8.18%, 6.45%, 5.88% and 3.7%, respectively). One notable feature of the studied populations is its high rate of consanguineous marriages. Considering this feature, determining the prevalent PKU mutations could be advantageous for designing screening and diagnostic panels in Iran.

Epidemiology, etiology, genetic variants in non- syndromic hearing loss in Iran: A systematic review and meta-analysis

OBJECTIVES

Hearing loss is one of the most common heterogeneous complicated disorders worldwide. We previously analyzed the results of published data on non-syndromic hearing loss in the Iranian population systematically. A broad range of genes is a challenge for molecular screening and clinical diagnosis in our populations on the ground of distinct genetics. The aim of this study was to analyze the role and frequency of the variants accountable for non-syndromic hearing loss (NSHL) in the Iranian population. These were identified with different methods including whole exome sequencing (WES), next-generation sequencing (NGS), targeted genomic enrichment and massively parallel sequencing (TGE + MPS), autozygosity mapping, STR markers, linkage analysis, and direct sequencing. This is the comprehensively study focusing on classifying 13 common NSHL genes according to their frequencies. Previous studies have not studied different regions and the Iranian population, and this is the definitive study on the topic.

METHODS

We searched Scopus, PubMed, Science Direct databases, and Google Scholar. After a systematic review of the evidence 95 studies were considered then 31 studies were eligible for meta-analysis. In total, 6995 families, 358 variants, and 117 novel variants were included. Statistical analyses were conducted using Stata SE version 11 software. The inverse variance method enjoyed combining data. Heterogeneity of the preliminary results was assessed using Q (Cochrane test), and I square index. Random effects or fixed models were applied to combine the results, relying on the degree of heterogeneity. Point and pooled prevalence of variants acting on different regions were illustrated by forest plots.

RESULTS

The total prevalence of at least one variant of GJB2 and SLC26A genes was estimated at 26% and 5%, respectively. Variant c.35delG accounted for 18% of the GJB2 variants while 1% of these variants were novel ones. The next most common variants in the GJB2 gene were c.109G>A at 3.5% and c.-23+1G>A at 2.3%. Moreover, the prevalence of GJB2 gene variants varied on average 0.002% from one region to another in Iran (p=0.849). Our meta-analysis also showed that the frequency of at least one variant of MYO15A varied between 1.2% and 12.5%. Corresponding prevalences for the other variants were as follows: ILDR1 (3.5%-3.7%), CDH23 (2%-10%), PJVK (1.4%-33%), TECTA (1.3%-6.7%), MYO6 (2%-4.8%), TMC1 (1.8%-2%), MYO7A (0.7%-5%), MARVELD2 (0.7-5%), OTOF (0.7%-4%), LRTOMT (0.7%-2.5%). Finally, we did not find any relationship between geographic area and the presence of these variants.

CONCLUSION

GJB2 gene variants were the most common cause of NSHL in Iran. Understanding the prevalence of NSHL gene frequency in Iran may be the foundation for future studies in an Iranian population which may lead to future NSHL therapy.

Tetrahydrobiopterin responsiveness in Phenylalanine hydroxylase deficient patients from North-east of Iran: Genotype-phenotype correlation, identification of a novel mutation and 7 new responsive genotypes

Phenylalanine hydroxylase enzyme defects result in a hereditary metabolic disorder called phenylketonuria. Sapropterin (tetrahydrobiopterin) is one of the treatment strategies for this disorder. Even though a correlation between genotype and BH4 responsiveness was established by earlier studies, a subset of mutations often presented inconsistent responses and/or phenotypes. Different genetic background is one of the potential reasons for this fact. In this study, the genotype of a total of 34 PAH deficient patients from Khorasan-Razavi providence in the north-east of Iran was obtained. Among this patients, 21 individuals took the 24 h and 48 h BH4 loading test and if the result was positive, their Phenylalanine tolerance was assessed. It is the first study of its type in patients from Iran to evaluate genotype role in predicting the most probable responsive individuals. The known pathogenic variant p.R169P and the novel variant p. Leu72_Asp75delinsTyr were first classified as responsive.Seven genotypes were reported as responsive for the first time. All patients carrying at least one pathogenic variant, which was previously reported as BH4 responsive, respond to BH4. Three patients with p.L48S, p.R261Q and p.A309V pathogenic variants were exceptions. There was no certain statistical correlation between genotype and response. Genotype and phenotype were significantly correlated and majority of patients with mild phenotype carried at least one non-null pathogenic variant. In Khorasan-Razavi province of Iran, patients with at least one non-null mutation are most probable to demonstrate mild phenotype and respond to BH4 phenotype.

The pathogenicity classification of PAH gene variants in the Iranian population

Till now not many studies have been conducted to classify PAH gene variants according to American College of Medical Genetics and Genomics (ACMG-AMP) guidelines. The aim of this study was to collect all PAH gene variants reported among Iranian population and investigate their pathogenicity based on ACMG-AMP guidelines. Systematic collection of PAH gene variants, verification of variants, in silico analysis, and application of ACMG-AMP guidelines were the main steps in performing the present study. A total of 267 unique variants were identified; according to ACMG-AMP guidelines, 90, 40, 71, 14, and 52 variants were classified as pathogenic (P), likely pathogenic (LP), variant of uncertain significance (VUS), likely benign (LB), and benign (B), respectively. The need to pay more attention to synonymous and missense variants with low or no impact on protein function as well as intronic variants, whether they are deep or are close to intron/exon boundaries, was a highlight of this study. Due to the fact that few functional studies are performed on these variants, it is suggested that they be analyzed first using bioinformatics tools, and if positive results are obtained, then functional studies can be designed.

Spectrum of PAH gene mutations and genotype-phenotype correlation in patients with phenylalanine hydroxylase deficiency from Turkey

OBJECTIVES

The aim of our study was to define the genotype-phenotype correlations of mutations in the PAH gene among the Turkey's Central Anatolian region.

METHODS

Demographic characteristics of 108 patients with hyperphenylalaninemia (HPA) and 94 patients whose diagnosis was confirmed by PAH gene analysis (Sanger DNA Sequence Analysis and Next-Generation Sequencing) were determined retrospectively. Blood phenylalanine levels were analyzed using the high-performance liquid chromatography method.

RESULTS

Mild HPA-not-requiring-treatment (NT) was found in 50.9% of the patients, and a classical phenylketonuria (PKU) phenotype was found in 25.9%. Forty-seven types of variants were identified. The predominant variants were p.Ala403Val (9.9%), p.Ala300Ser (9.4%), and c.1066-11G>A (splicing) (9.4%). Missense mutations accounted for 68% of mutations and attenuated the clinical impact; splice variations were found in 14.8% of cases with severe features. The p.Thr380Met allele was specific to the mild HPA-NT group. The c.1066-11G>A (splicing) allele was associated with classical PKU, whereas the p.Arg408Trp allele was linked to severe symptoms. Three variations of unknown clinical significance were discovered: c.706+4A>T (splicing), c.843-5T>C (splicing), and p.Thr323=. Of these variants, the patient who was homozygous for the c.843-5T>C (splicing) allele related to the classical PKU phenotype. 70% of the patients who underwent tetrahydrobiopterin (BH4) test were responsive. Phenotypes that responded to BH4 treatment were mostly mild phenotypes.

CONCLUSIONS

The PAH genotype is the main factor that determines the phenotype of PKU. Establishing the relationship between the identified genetic mutations and phenotypic characteristics will provide very important data for each patient in terms of the specific management style.

Evaluation of patients with phenylalanine metabolism disorder: a single center experience

AIM

The aim is to evaluate the clinical, demographic and laboratory data of the patients we followed up with phenylalanine metabolism disorder.

MATERIALS AND METHODS

In this study, patients with phenylalanine metabolism disorder who applied to Bursa Uludag University Faculty of Medicine, Department of Pediatrics, Pediatric Metabolism Department between 2011 and 2021 were retrospectively examined. The files of 397 patients who were followed up in our pediatric metabolism outpatient clinic and were found to have phenylalanine metabolism disorder by plasma phenylalanine level and molecular genetic analysis were evaluated.

RESULTS

According to the highest plasma phenylalanine levels at admission, mild hyperphenylalaninemia phenotype constituted the largest group of 397 patients with 282 cases (71.1%), while the least common phenotype was malignant phenylketonuria (BH4 metabolism disorder) with four patients (1.0%). The number of patients with classical phenylketonuria was 90 (22.6%). 61 (62.8%) of 97 phenylalanine metabolism disorder cases who underwent BH4 loading test had a response. The mean phenylalanine level of the patients was 3.62 ± 1.31 mg/dL in mild hyperphenylalaninemia, 7.98 ± 3.99 mg/dL in mild phenylketonuria and 11.71 ± 4.39 mg/dL in classical phenylketonuria. While 241 (76%) of 317 patients younger than 8 years old were in the well-controlled group, 76 (24%) were in the poorly-controlled group. While 41 (53.9%) of 76 patients older than 8 years of age were in the well-controlled group, 35 (46.1%) were in the poorly-controlled group.

CONCLUSIONS

In our study, the largest patient group consisted of patients with mild hyperphenylalaninemia, and the least common phenotype was mild phenylketonuria.

Spectrum of PAH gene mutations in 1547 phenylketonuria patients from Iran: a comprehensive systematic review

As one of the highest prevalence rates in the world, the prevalence of Phenylketonuria (PKU) in Iran has been estimated at 16.5 per 100,000 neonates. The objective of this study was to evaluate the spectrum and frequency of mutations of the phenylalanine hydroxylase (PAH) gene in Iranian PKU patients. A systematic review was carried out on previous studies on PAH gene mutations in Iranian PKU patients. A complete search was carried out on the on-line databases of Scopus, Web of Science, PubMed/Medline, ProQuest, Science Direct, Magiran, SID and the search engine Google Scholar. The keywords of Phenylketonuria, PKU, Phenylalanine Hydroxylase, PAH, and Iran, as well as their Persian equivalents, in all possible combinations were used. Finally, a total of 21 eligible articles with a sample size of 1547 Iranian PKU patients, published between 2003 and 2020, were included in our systematic review. A total of 129 different PAH gene mutations including, IVS10-11G > A (c.1066-11G > A) (19.23%), p.R261Q (c.782G > A) (7.63%), p.P281L (c.842C > T) (6.24%), IVS2 + 5G > C (c.168 + 5G > C) (5.75%), p.R243* (c.727C > T) (3.59%), IVS9 + 5G > A (c.969 + 5G > A) (2.84%), p.R176* (c.526C > T) (2.42%), p.Lys363Nfs*37 (c.1089delG) (2.13%), IVS11 + 1G > C (c.1199 + 1G > C) (2.07%) and p.L48S (c.143 T > C) (2.04%) were identified. The spectrum and frequency of mutations observed in Iran were closer to those observed in the Mediterranean countries. Our results are valuable in planning panel-based studies in provinces with incomplete data on PAH gene mutations. This study is a good reference for genetic counselors and physicians who advise couples in making decisions to maintain or terminate a pregnancy.

Genetic variants of the phenylalanine hydroxylase gene in patients with phenylketonuria in the northeast of Iran

Background Phenylketonuria (PKU) is a common metabolic disorder with great burden if left untreated or undiagnosed. Genetic variations in the phenylalanine hydroxylase (PAH) gene may be widely varied across different regions of a country. By knowing the most common mutations, diagnostic work-ups will be offered sooner and with lower costs for patients. The present study defines the most common genetic variations in the PAH gene in Khorasan province of Iran. Methods The present cross-sectional study took place in Khorasan province of Iran within a 6-year period starting from 2012 to 2018. Every patient who had been referred as suspicious PKU cases or referred for prenatal diagnosis was included in the present study. Results A total number of 122 individuals with a mean age of 26.22 years were enrolled in the present study. The most frequent genetic variations in the PAH gene were c.1066-11G > A and c.143 T > C. Exon 7 carried the most genetic variations compared to any single exon. Also, three patients had compound heterozygous status for c.727 C > T/c.1066-11 G > A in exon 7 and 11 of the PAH gene. Conclusions Mutations in the PAH gene are widely varied among different populations, and our results confirmed this fact. Determination of the most prevalent mutations and polymorphisms in each region will reduce the time and cost of diagnosing such preventable diseases and will therefore reduce the disease burden.

Population and evolutionary genetics of the PAH locus to uncover overdominance and adaptive mechanisms in phenylketonuria: Results from a multiethnic study

BACKGROUND

Phenylketonuria (PKU) is the most common inborn error of amino acid metabolism in Europe. The reasons underlying the high prevalence of heterozygous carriers are not clearly understood. We aimed to look for pathogenic PAH variant enrichment according to geographical areas and patients' ethnicity using a multiethnic nationwide cohort of patients with PKU in France. We subsequently appraised the population differentiation, balancing selection and the molecular evolutionary history of the PAH locus.

METHODS

The French nationwide PKU study included patients who have been referred at the national level to the University Hospital of Nancy, and for whom a molecular diagnosis of phenylketonuria was made by Sanger sequencing. We performed enrichment analyses by comparing alternative allele frequencies using Fisher's exact test with Bonferroni adjustment. We estimated the amount of genetic differentiation among populations using Wright's fixation index (Fst). To estimate the molecular evolutionary history of the PAH gene, we performed phylogenetic and evolutionary analyses using whole-genome and exome-sequencing data from healthy individuals and non-PKU patients, respectively. Finally, we used exome-wide association study to decipher potential genetic loci associated with population divergence on PAH.

FINDINGS

The study included 696 patients and revealed 132 pathogenic PAH variants. Three geographical areas showed significant enrichment for a pathogenic PAH variant: North of France (p.Arg243Leu), North-West of France (p.Leu348Val), and Mediterranean coast (p.Ala403Val). One PAH variant (p.Glu280Gln) was significantly enriched among North-Africans (OR = 23·23; 95% CI: 9·75-55·38). PAH variants exhibiting a strong genetic differentiation were significantly enriched in the 'Biopterin_H' domain (OR = 6·45; 95% CI: 1·99-20·84), suggesting a balancing selection pressure on the biopterin function of PAH. Phylogenetic and timetree analyses were consistent with population differentiation events on European-, African-, and Asian-ancestry populations. The five PAH variants most strongly associated with a high selection pressure were phylogenetically close and were located within the biopterin domain coding region of PAH or in its vicinity. Among the non-PAH loci potentially associated with population divergence, two reached exome-wide significance: SSPO (SCO-spondin) and DBH (dopamine beta-hydroxylase), involved in neuroprotection and metabolic adaptation, respectively.

INTERPRETATION

Our data provide evidence on the combination of evolutionary and adaptive events in populations with distinct ancestries, which may explain the overdominance of some genetic variants on PAH.

FUNDING

French National Institute of Health and Medical Research (INSERM) UMR_S 1256.

Development and validation of a novel panel of 16 STR markers for simultaneous diagnosis of β-thalassemia, aneuploidy screening, maternal cell contamination detection and fetal sample authenticity in PND and PGD/PGS cases

Prenatal diagnosis (PND) may be complicated with sample mix-up; maternal cell contamination, non-paternity and allele drop out at different stages of diagnosis. Aneuploidy screening if combined with PND for a given single gene disorder, can help to detect any common aneuploidy as well as aiding sample authenticity and other probable complications which may arise during such procedures. This study was carried out to evaluate the effectiveness of a novel panel of STR markers combined as a multiplex PCR kit (HapScreen™ kit) for the detection of β-thalassemia, aneuploidy screening, ruling in/out maternal cell contamination (MCC), and sample authenticity. The kit uses 7 STR markers linked to β-globin gene (HBB) as well as using 9 markers for quantitative analysis of chromosomes 21, 18, 13, X and Y. Selection of the markers was to do linkage analysis with β-globin gene, segregation analysis and to perform a preliminary aneuploidy screening of fetal samples respectively. These markers (linked to the β-globin gene) were tested on more than 2185 samples and showed high heterozygosity values (68.4-91.4%). From 2185 fetal cases we found 3 cases of non-paternity, 5 cases of MCC, one case of sample mix-up and one case of trisomy 21 which otherwise may have end up to misdiagnosis. This kit was also successfully used on 231 blastomeres for 29 cases of pre-implantation genetic diagnosis (PGD) and screening (PGS). The markers used for simultaneous analysis of haplotype segregation and aneuploidy screening proved to be very valuable to confirm results obtained from direct mutation detection methods (i.e. ARMS, MLPA and sequencing) and aneuploidy screening.