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Khaghani F, Eshraghi P, Hamzehloei T. 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. Eur J Med Genet 2022; 65:104536. [PMID: 35690318 DOI: 10.1016/j.ejmg.2022.104536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/03/2022] [Accepted: 06/05/2022] [Indexed: 11/03/2022]
Abstract
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.
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Affiliation(s)
- Faeze Khaghani
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Peyman Eshraghi
- Department of Pediatric and Endocrinology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tayebeh Hamzehloei
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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2
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Çınar M, Kılıç Yıldırım G, Kocagil S, Çilingir O. Spectrum of PAH gene mutations and genotype-phenotype correlation in patients with phenylalanine hydroxylase deficiency from Turkey. J Pediatr Endocrinol Metab 2022; 35:639-647. [PMID: 35355500 DOI: 10.1515/jpem-2022-0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/07/2022] [Indexed: 11/15/2022]
Abstract
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.
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Affiliation(s)
- Müge Çınar
- Pediatrics, Bozüyük State Hospital, Bilecik, Turkey
| | - Gonca Kılıç Yıldırım
- Department of Paediatrics, Eskisehir Osmangazi University Faculty of Medicine, Division of Child Nutrition and Metabolism, Eskisehir, Turkey
- Eskisehir Osmangazi University Faculty of Medicine, Meselik Campuse, Odunpazari, Turkey
| | - Sinem Kocagil
- Eskisehir Osmangazi University Faculty of Medicine, Meselik Campuse, Odunpazari, Turkey
- Department of Genetics and Genomics Medicine, Eskisehir Osmangazi University Faculty of Medicine, Eskisehir, Turkey
| | - Oğuz Çilingir
- Eskisehir Osmangazi University Faculty of Medicine, Meselik Campuse, Odunpazari, Turkey
- Department of Genetics and Genomics Medicine, Eskisehir Osmangazi University Faculty of Medicine, Eskisehir, Turkey
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3
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Jin X, Yan Y, Zhang C, Tai Y, An L, Yu X, Zhang L, Hao S, Cao X, Yin C, Ma X. Identification of novel deep intronic PAH gene variants in patients diagnosed with phenylketonuria. Hum Mutat 2021; 43:56-66. [PMID: 34747549 DOI: 10.1002/humu.24292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 10/21/2021] [Accepted: 10/28/2021] [Indexed: 12/17/2022]
Abstract
Phenylketonuria (PKU) is caused by phenylalanine hydroxylase (PAH) gene variants. Previously, 94.21% of variants were identified using Sanger sequencing and multiplex ligation-dependent probe amplification. To investigate the remaining variants, we performed whole-genome sequencing for four patients with PKU and unknown genotypes to identify deep intronic or structural variants. We identified three novel heterozygous variants (c.706+368T>C, c.1065+241C>A, and c.1199+502A>T) in a deep PAH gene intron. We detected a c.1199+502A>T variant in 60% (6/10) of PKU patients with genetically undetermined PKU. In silico predictions indicated that the three deep variants may impact splice site selection and result in the inclusion of a pseudo-exon. A c.1199+502A>T PAH minigene and reverse transcription PCR (RT-PCR) on blood RNA from a PKU patient with biallelic variants c.1199+502A>T and c.1199G>A confirmed that the c.1199+502A>T variant may strengthen the predicted branch point and leads to the inclusion of a 25-nt pseudo-exon in the PAH mRNA. Reverse transcription polymerase chain reaction (RT-PCR) on the minigene revealed that c.706+368T>C may create an SRSF2 (SC35) binding site via a 313-nt pseudo-exon, whereas c.1065+241C>A may produce an 81-nt pseudo-exon that strengthens the predicted SRSF1 (SF2/ASF) binding site. These results augment current knowledge of PAH genotypes and show that deep intronic analysis of PAH can genetically diagnose PKU.
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Affiliation(s)
- Xiaohua Jin
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
| | - Yousheng Yan
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Chuan Zhang
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China.,Gansu Province Medical Genetics Center, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Ya Tai
- Department of Obstetrics and Gynecology, Peking University International Hospital, Beijing, China
| | - Lisha An
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
| | - Xinyou Yu
- Department of Prenatal Diagnosis Center, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Linlin Zhang
- Clinical Lab, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shengju Hao
- Gansu Province Medical Genetics Center, Gansu Provincial Maternity and Child-Care Hospital, Lanzhou, China
| | - Xiaofang Cao
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
| | - Chenghong Yin
- Prenatal Diagnostic Center, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Xu Ma
- National Research Institute for Family Planning, Beijing, China.,National Human Genetic Resources Center, Beijing, China
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4
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Nemati H, Yousefi SK, Pourvatan N, Aparviz R, Farzaneh P, Koohpar ZK, Safari F, Asl AS, Ranji N. Mutation analysis of phenylketonuria in the North of Iran. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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5
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Lopez A, Havranek B, Papadantonakis GA, Islam SM. In silico screening and molecular dynamics simulation of deleterious PAH mutations responsible for phenylketonuria genetic disorder. Proteins 2021; 89:683-696. [PMID: 33491267 DOI: 10.1002/prot.26051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/08/2021] [Accepted: 01/21/2021] [Indexed: 12/23/2022]
Abstract
Phenylketonuria (PKU) is a genetic disorder that if left untreated can lead to behavioral problems, epilepsy, and even mental retardation. PKU results from mutations within the phenylalanine-4-hydroxylase (PAH) gene that encodes for the PAH protein. The study of all PAH causing mutations is improbable using experimental techniques. In this study, a collection of in silico resources, sorting intolerant from tolerant, Polyphen-2, PhD-SNP, and MutPred were used to identify possible pathogenetic and deleterious PAH non-synonymous single nucleotide polymorphisms (nsSNPs). We identified two variants of PAH, I65N and L311P, to be the most deleterious and disease causing nsSNPs. Molecular dynamics (MD) simulations were carried out to characterize these point mutations on the atomic level. MD simulations revealed increased flexibility and a decrease in the hydrogen bond network for both mutants compared to the native protein. Free energy calculations using the MM/GBSA approach found that BH4 , a drug-based therapy for PKU patients, had a higher binding affinity for I65N and L311P mutants compared to the wildtype protein. We also identify important residues in the BH4 binding pocket that may be of interest for the rational drug design of other PAH drug-based therapies. Lastly, free energy calculations also determined that the I65N mutation may impair the dimerization of the N-terminal regulatory domain of PAH.
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Affiliation(s)
- Andrea Lopez
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Brandon Havranek
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, USA
| | | | - Shahidul M Islam
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois, USA
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6
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Molecular characterization of Thai patients with phenylalanine hydroxylase deficiency and in vitro functional study of two novel PAH variants. Mol Biol Rep 2021; 48:2063-2070. [PMID: 33677757 DOI: 10.1007/s11033-021-06163-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/15/2021] [Indexed: 10/22/2022]
Abstract
Phenylketonuria (PKU) is an autosomal recessive amino acid metabolism disorder caused by variants in the gene encoding phenylalanine hydroxylase (PAH; EC1.14.16.1). This study aimed to assess the specific heterogeneity of PAH variants found in Thai population as well as evaluate enzyme activity and expression of novel variants. PAH gene from 13 patients was analyzed by PCR amplification and direct Sanger-sequencing of 13 exons of the coding region. The novel variants were transiently transfected in COS-7 cells for functional verification. Eleven different PAH variants were identified: all pathogenic variants were missense variants, of which the most frequent variant was p.R169L, accounting for 24% (6/25) of all identified alleles. Two novel variants p.R169L and p.Y317N and previously reported variants with mutated residues at the same positions (p.R169H and p.Y317H) were expressed in COS-7 cells. These showed mildly impaired residual activity levels (42.3-63.1% of wild type), while the protein levels were well expressed (82.8-110%), except for p.R169L, which showed decreased protein expression of 55.7% compared to the wild type enzyme. All subjects with p.R169L identified in at least one of pathogenic alleles (one case is homozygous) had a metabolic phenotype of mild hyperphenylalaninemia (HPA). Our data has expanded the information on the genetic heterogeneity of Thai patients with PAH deficiency. This finding emphasizes the importance of genotyping in patients with HPA, and in vitro studies can provide additional information for prediction of phenotype.
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7
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Tao Y, Han D, Shen H, Li X. Spectrum of PAH gene mutations and genotype-phenotype correlation in patients with phenylalanine hydroxylase deficiency from Shanxi province. Brain Dev 2021; 43:220-229. [PMID: 32893076 DOI: 10.1016/j.braindev.2020.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 08/04/2020] [Accepted: 08/18/2020] [Indexed: 01/12/2023]
Abstract
BACKGROUND Phenylalanine hydroxylase deficiency (PAHD) is an autosomal recessive inborn error that affects phenylalanine (Phe) metabolism. It has a complex phenotype with many variants and genotypes among different populations. Shanxi province is a high-prevalence area of PAHD in China. METHODS In this study, eighty-nine PAHD patients were subjected to genetic testing using Sanger sequencing, followed by multiplex ligation-dependent probe amplification analysis (MLPA). Allelic and genotypic phenotype values (APV and GPV, respectively) were used for genotype-based phenotypic prediction. RESULTS Fifty-one types of variants, including three novel forms, were identified. The predominant variant was p.R243Q (22.09%), followed by p.R53H (10.47%), p.EX6-96A > G (9.30%), p.V399V (5.23%) and p.R413P (3.49%). Notably, mild hyperphenylalaninemia (MHP) has a high prevalence in this region (up to 45.76%), and the variant p.R53H was solely observed in patients of MHP. According to the genotype-phenotype prediction, the APV/GPV system was well correlated with the metabolic phenotype of most PAHD patients. CONCLUSION We have systematically constructed the mutational and phenotypic spectrum of PAH in Shanxi province. Hence, this study will help to further understand the genotype-phenotype associations in PAHD patients, and it may offer more reliable genetic counseling and management.
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Affiliation(s)
- Yilun Tao
- Medical Genetic Center, Changzhi Maternal and Child Health Care Hospital, 38 Weiyuanmen Road, Changzhi, Shanxi 046000, China
| | - Dong Han
- Medical Genetic Center, Changzhi Maternal and Child Health Care Hospital, 38 Weiyuanmen Road, Changzhi, Shanxi 046000, China
| | - Huiyi Shen
- Medical Genetic Center, Changzhi Maternal and Child Health Care Hospital, 38 Weiyuanmen Road, Changzhi, Shanxi 046000, China
| | - Xiaoze Li
- Medical Genetic Center, Changzhi Maternal and Child Health Care Hospital, 38 Weiyuanmen Road, Changzhi, Shanxi 046000, China.
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8
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Huang YQ, Yang F, Zhu JP, Qiu JG, Li YL, Zhang L, Li HF, Zhang YL, Qin SY. Identification and characterization of a novel deletion in the phenylalanine hydroxylase gene of a Chinese patient. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Zhu Z, Gu J, Genchev GZ, Cai X, Wang Y, Guo J, Tian G, Lu H. Improving the Diagnosis of Phenylketonuria by Using a Machine Learning-Based Screening Model of Neonatal MRM Data. Front Mol Biosci 2020; 7:115. [PMID: 32733913 PMCID: PMC7358370 DOI: 10.3389/fmolb.2020.00115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/18/2020] [Indexed: 12/03/2022] Open
Abstract
Phenylketonuria (PKU) is a common genetic metabolic disorder that affects the infant's nerve development and manifests as abnormal behavior and developmental delay as the child grows. Currently, a triple–quadrupole mass spectrometer (TQ-MS) is a common high-accuracy clinical PKU screening method. However, there is high false-positive rate associated with this modality, and its reduction can provide a diagnostic and economic benefit to both pediatric patients and health providers. Machine learning methods have the advantage of utilizing high-dimensional and complex features, which can be obtained from the patient's metabolic patterns and interrogated for clinically relevant knowledge. In this study, using TQ-MS screening data of more than 600,000 patients collected at the Newborn Screening Center of Shanghai Children's Hospital, we derived a dataset containing 256 PKU-suspected cases. We then developed a machine learning logistic regression analysis model with the aim to minimize false-positive rates in the results of the initial PKU test. The model attained a 95–100% sensitivity, the specificity was improved 53.14%, and positive predictive value increased from 19.14 to 32.16%. Our study shows that machine learning models may be used as a pediatric diagnosis aid tool to reduce the number of suspected cases and to help eliminate patient recall. Our study can serve as a future reference for the selection and evaluation of computational screening methods.
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Affiliation(s)
- Zhixing Zhu
- Center for Biomedical Informatics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Shanghai, China
| | - Jianlei Gu
- Center for Biomedical Informatics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Shanghai, China.,Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China
| | - Georgi Z Genchev
- Center for Biomedical Informatics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China.,Bulgarian Institute for Genomics and Precision Medicine, Sofia, Bulgaria
| | - Xiaoshu Cai
- Center for Biomedical Informatics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Shanghai, China
| | - Yangmin Wang
- Newborn Screening Center, Shanghai Children's Hospital, Shanghai, China
| | - Jing Guo
- Newborn Screening Center, Shanghai Children's Hospital, Shanghai, China
| | - Guoli Tian
- Newborn Screening Center, Shanghai Children's Hospital, Shanghai, China
| | - Hui Lu
- Center for Biomedical Informatics, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Engineering Research Center for Big Data in Pediatric Precision Medicine, Shanghai, China.,Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China
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10
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Yan Y, Jin X, Wang X, Zhang C, Zhang Q, Zheng L, Feng X, Hao S, Gao H, Ma X. Screening of PAH Common Mutations in Chinese Phenylketonuria Patients Using iPLEX MALDI-TOF MS. ACS OMEGA 2020; 5:1805-1812. [PMID: 32039316 PMCID: PMC7003239 DOI: 10.1021/acsomega.9b02955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
Phenylketonuria (PKU) is caused by phenylalanine hydroxylase (PAH) gene variants. Previous research has identified some PAH mutation hotspots in Chinese patients with PKU. In this study, we introduce a novel MassArray panel for screening the 29 common PAH gene mutations in Chinese patients using iPLEX MALDI-TOF MS. 105 Patients with PKU and known PAH gene mutations were genotyped using this MassArray panel. All of the 29 mutations screened were detected, and MassArray panel results were consistent with those obtained by Sanger sequencing. Fifty patients newly diagnosed with PKU were recruited in the double-blind experiment. PAH gene variants were detected in these 50 patients using the MassArray panel, and the results were verified with Sanger sequencing and Multiplex Ligation-dependent Probe Amplification (MLPA) methods. Our results show that the mutation detection rate using the MassArray panel with 29 mutations is 74% (95% CI, 65-83%), and the clinical genetic diagnosis rate is 54% (95% CI, 40-68%). This panel can be used as a high throughput, low cost, and rapid method for screening and diagnosing PAH gene mutations. The establishment of this approach provides proof-of-concept for future large-scale PAH mutation carrier screening in areas with high rates of PKU.
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Affiliation(s)
- Yousheng Yan
- National
Research Institute for Family Planning, Beijing 100081, China
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
- Peking
University International Hospital, Beijing 102206, China
| | - Xiaohua Jin
- National
Research Institute for Family Planning, Beijing 100081, China
| | - Xing Wang
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
| | - Chuan Zhang
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
| | - Qinhua Zhang
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
| | - Lei Zheng
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
| | - Xuan Feng
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
| | - Shengju Hao
- Gansu
Province Medical Genetics Center, Gansu
Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
| | - Huafang Gao
- National
Research Institute for Family Planning, Beijing 100081, China
| | - Xu Ma
- National
Research Institute for Family Planning, Beijing 100081, China
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11
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Yan Y, Zhang C, Jin X, Zhang Q, Zheng L, Feng X, Hao S, Gao H, Ma X. Mutation spectrum of PAH gene in phenylketonuria patients in Northwest China: identification of twenty novel variants. Metab Brain Dis 2019; 34:733-745. [PMID: 30747360 DOI: 10.1007/s11011-019-0387-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/20/2019] [Indexed: 10/27/2022]
Abstract
This study was performed to analyze the mutational spectrum of the phenylalanine hydroxylase (PAH) gene in phenylketonuria (PKU) patients in Northwest China, to identify mutational hot spots, and to determine the correlation between variants and clinical phenotypes of PKU. A large cohort of 475 PKU families in Northwest China was enrolled to analyze PAH gene variants using Sanger sequencing, Multiplex ligation-dependent probe amplification (MLPA), and gap-PCR. Bioinformatics software was used to predict the pathogenicity of novel variants and analyze the correlations between PAH gene variants and phenotypes of PKU patients. A total of 895 variants were detected in the 950 alleles of 475 patients with PKU (detection rate: 94.21%), 20 of which were novel variants. Other 108, previously known variants, were also identified, with the three most frequent variants being p.Arg243Gln (14.00%), c.611A > G (5.58%), and p.Tyr356* (4.95%). Seven different large deletion/duplication variants were identified by the MLPA method, including the large deletion c.-4163_-406del3758 with high frequency. A correlation analysis between patient phenotype and gene variant frequency showed that p.Arg53His and p.Gln419Arg were correlated with mild hyperphenylalaninemia (MHP). In conclusion, the mutational spectrum underlying PKU in Northwest China was established for the first time. Functional analysis of 20 novel PAH gene variants enriched the PAH gene mutational spectrum. Correlation analysis between variants frequencies in compound heterozygous patients and phenotype severity is helpful for phenotypic prediction.
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Affiliation(s)
- Yousheng Yan
- Graduate School of Peking Union Medical College, Beijing, 100730, China
- National Research Institute for Health and Family Planning, No. 12 Dahuisi Road, Beijing, 100081, China
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, 730050, China
| | - Chuan Zhang
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, 730050, China
| | - Xiaohua Jin
- Graduate School of Peking Union Medical College, Beijing, 100730, China
- National Research Institute for Health and Family Planning, No. 12 Dahuisi Road, Beijing, 100081, China
| | - Qinhua Zhang
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, 730050, China
| | - Lei Zheng
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, 730050, China
| | - Xuan Feng
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, 730050, China
| | - Shengju Hao
- Gansu Province Medical Genetics Center, Gansu Province Maternal and Child Health Care Hospital, Lanzhou, 730050, China
| | - Huafang Gao
- Graduate School of Peking Union Medical College, Beijing, 100730, China.
- National Research Institute for Health and Family Planning, No. 12 Dahuisi Road, Beijing, 100081, China.
| | - Xu Ma
- Graduate School of Peking Union Medical College, Beijing, 100730, China.
- National Research Institute for Health and Family Planning, No. 12 Dahuisi Road, Beijing, 100081, China.
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12
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Shirzadeh T, Saeidian AH, Bagherian H, Salehpour S, Setoodeh A, Alaei MR, Youssefian L, Samavat A, Touati A, Fallah MS, Vahidnezhad H, Karimipoor M, Azadmehr S, Raeisi M, Bandehi Sarhadi A, Zafarghandi Motlagh F, Jamali M, Zeinali Z, Abiri M, Zeinali S. Molecular genetics of a cohort of 635 cases of phenylketonuria in a consanguineous population. J Inherit Metab Dis 2018; 41:1159-1167. [PMID: 30159852 DOI: 10.1007/s10545-018-0228-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/09/2018] [Accepted: 06/26/2018] [Indexed: 11/28/2022]
Abstract
Phenylketonuria (PKU) is an inborn error of amino acid metabolism caused by mutations in the phenylalanine hydroxylase (PAH) gene, characterized by intellectual deficit and neuropsychiatric complications in untreated patients with estimated frequency of about one in 10,000 to 15,000 live births. PAH deficiency can be detected by neonatal screening in nearly all cases with hyperphenylalaninemia on a heel prick blood spot. Molecular testing of the PAH gene can then be performed in affected family members. Herein, we report molecular study of 635 patients genetically diagnosed with PKU from all ethnicities in Iran. The disease-causing mutations were found in 611 (96.22%) of cases. To the best of our knowledge, this is the most comprehensive molecular genetics study of PKU in Iran, identifying 100 distinct mutations in the PAH gene, including 15 previously unreported mutations. Interestingly, we found unique cases of PKU with uniparental disomy, germline mosaicism, and coinheritance with another Mendelian single-gene disorder that provides new insights for improving the genetic counseling, prenatal diagnosis (PND), and/or pre-implantation genetic diagnosis (PGD) for the inborn error of metabolism group of disorders.
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Affiliation(s)
- Tina Shirzadeh
- Kawsar Human Genetics Research Center, 41 Majlesi St., Vali Asr St., Tehran, 1595645513, Iran
| | - Amir Hossein Saeidian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Genetic, Genomics and Cancer Biology PhD Program, Thomas Jefferson University, Philadelphia, PA, USA
| | - Hamideh Bagherian
- Kawsar Human Genetics Research Center, 41 Majlesi St., Vali Asr St., Tehran, 1595645513, Iran
| | - Shadab Salehpour
- Department of Pediatric Endocrinology and Metabolism, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Aria Setoodeh
- Growth and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran
- Department of Pediatrics, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Alaei
- Department of Pediatric Endocrinology and Metabolism, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Leila Youssefian
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Genetic, Genomics and Cancer Biology PhD Program, Thomas Jefferson University, Philadelphia, PA, USA
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ashraf Samavat
- Genetics Office, CDC, Ministry of Health of Iran, Tehran, Iran
| | - Andrew Touati
- Drexel University College of Medicine, Philadelphia, PA, USA
| | - Mohammad-Sadegh Fallah
- Kawsar Human Genetics Research Center, 41 Majlesi St., Vali Asr St., Tehran, 1595645513, Iran
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Karimipoor
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Sarah Azadmehr
- Kawsar Human Genetics Research Center, 41 Majlesi St., Vali Asr St., Tehran, 1595645513, Iran
| | - Marzieh Raeisi
- Research Institute for Endocrine Science, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of cellular and molecular biology, Islamic Azad University North Tehran branch, Tehran, Iran
| | - Ameneh Bandehi Sarhadi
- Kawsar Human Genetics Research Center, 41 Majlesi St., Vali Asr St., Tehran, 1595645513, Iran
| | | | - Mojdeh Jamali
- Kawsar Human Genetics Research Center, 41 Majlesi St., Vali Asr St., Tehran, 1595645513, Iran
| | - Zahra Zeinali
- Kawsar Human Genetics Research Center, 41 Majlesi St., Vali Asr St., Tehran, 1595645513, Iran
| | - Maryam Abiri
- Department of Medical Genetics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Sirous Zeinali
- Kawsar Human Genetics Research Center, 41 Majlesi St., Vali Asr St., Tehran, 1595645513, Iran.
- Department of Molecular Medicine, Biotech Research Center, Pasteur Institute of Iran, Tehran, Iran.
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13
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Liu Y, Dong Z, Yu S. Late-diagnosed phenylketonuria mimicking x-linked adrenoleukodystrophy with heterozygous mutations of the PAH Gene: A case report and literature review. Clin Neurol Neurosurg 2018; 171:151-155. [DOI: 10.1016/j.clineuro.2018.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 05/12/2018] [Accepted: 06/09/2018] [Indexed: 11/26/2022]
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14
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Li N, He C, Li J, Tao J, Liu Z, Zhang C, Yuan Y, Jiang H, Zhu J, Deng Y, Guo Y, Li Q, Yu P, Wang Y. Analysis of the genotype-phenotype correlation in patients with phenylketonuria in mainland China. Sci Rep 2018; 8:11251. [PMID: 30050108 PMCID: PMC6062512 DOI: 10.1038/s41598-018-29640-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 07/13/2018] [Indexed: 11/22/2022] Open
Abstract
Mutations in the gene encoding phenylalanine hydroxylase (PAH) are associated with various degrees of phenylketonuria (PKU). The aim of our study was to define the genotype-phenotype correlations of mutations in the PAH gene that cause phenylketonuria (PKU) among the Chinese mainland population. Mutations in the PAH gene were analysed by next-generation sequencing, and a genotype-phenotype correlation analysis was performed in 1079 patients. Fifteen “null + null” genotypes, including four homoallelic and eleven heteroallelic genotypes, were clearly associated with classic PKU. Five functionally hemizygous (p.E280K, p.R252Q, p.E56D, p.S310F and p.T372R) and four compound heterozygous (p.T278I/p.S359L, p.R408W/p.R243Q, p.F161S/p.R243Q and p.F161S/p.R413P) genotypes were clearly associated with classic PKU. Ten functionally hemizygous genotypes, p.G257V, p.R158W, p.L255S, p.G247V, p.F161S, p.R158Q, p.V388M, p.I65T, p.I324N and p.R400K, were frequently associated with classic PKU. Three functionally hemizygous genotypes, p.P147L, p.I95del and p.F331S, and four compound heterozygous genotypes, p.G257V/p.R408Q, p.A434D/p.R413P, p.R243Q/p.A47E and p.R241C/p.G239D, were consistently correlated with mild PKU. Three functionally hemizygous genotypes, p.H107R, p.Q419R and p.F392I, and nine compound heterozygous genotypes (p.G312V/p.R241C, p.R243Q/p.V230I, p.R243Q/p.A403V, p.R243Q/p.Q419R, p.R243Q/p.R53H, p.R243Q/p.H107R, p.R241C/p.R408Q, p.R241C/p.H220P and p.R53H/p.R400K) were consistent with mild hyperphenylalaninaemia (MHP). Our study provides further support for the hypothesis that the PAH genotype is the main factor that determines the phenotype of PKU.
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Affiliation(s)
- Nana Li
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Chunhua He
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Jing Li
- Laboratory of Translational Medicine, Chinese PLA General Hospital, Beijing, China
| | - Jing Tao
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Zhen Liu
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Chunyan Zhang
- Laboratory of Translational Medicine, Chinese PLA General Hospital, Beijing, China
| | - Yuan Yuan
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, 300308, China
| | - Hui Jiang
- BGI-Shenzhen, Shenzhen, 518103, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jun Zhu
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Ying Deng
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Yixiong Guo
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Qintong Li
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Ping Yu
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China. .,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China.
| | - Yanping Wang
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China. .,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China.
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15
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Vieira Neto E, Laranjeira F, Quelhas D, Ribeiro I, Seabra A, Mineiro N, d. M. Carvalho L, Lacerda L, G. Ribeiro M. Mutation analysis of the PAH gene in phenylketonuria patients from Rio de Janeiro, Southeast Brazil. Mol Genet Genomic Med 2018; 6:575-591. [PMID: 29749107 PMCID: PMC6081236 DOI: 10.1002/mgg3.408] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 03/29/2018] [Accepted: 04/06/2018] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Phenylketonuria (PKU) is an autosomal recessive disease resulting from mutations in the PAH gene. Most of the patients are compound heterozygotes, and genotype is a major factor in determining the phenotypic variability of PKU. More than 1,000 variants have been described in the PAH gene. Rio de Janeiro's population has a predominance of Iberian, followed by African and Amerindian ancestries. It is expected that most PKU variants in this Brazilian state have originated in the Iberian Peninsula. However, rare European, African or pathogenic variants that are characteristic of the admixed population of the state might also be found. METHODS A total of 102 patients were included in this study. Genomic DNA was isolated from dried blood spots. Sanger sequencing was used for PAH gene variant identification. Deletions and duplications were also screened using MLPA analysis. Haplotypes were also determined. RESULTS Nine (8.8%) homozygous and 93 (91.2%) compound heterozygous patients were found. The spectrum included 37 causative mutations. Missense, nonsense, and splicing pathogenic variants corresponded to 63.7%, 2.9%, and 22.6% of the mutant alleles, respectively. Large (1.5%), and small deletions, inframe (5.4%) and with frameshift (3.9%), comprised the remainder. The most frequent pathogenic variants were: p.V388M (12.7%), p.R261Q (11.8%), IVS10-11G>A (10.3%), IVS2+5G>C (6.4%), p.S349P (6.4%), p.R252W (5.4%), p.I65T (4.4%), p.T323del (4.4%), and p.P281L (3.4%). One novel variant was detected: c.934G>T (p.G312C) [rs763115697]. CONCLUSION The three most frequent pathogenic variants in our study (34.8% of the alleles) were also the most common in other Brazilian states, Portugal, and Spain (p.V388M, p.R261Q, IVS10-11G>A), corroborating that the Iberian Peninsula is the major source of PAH mutations in Rio de Janeiro. Pathogenic variants that have other geographical origins, such IVS2+5G>C, p.G352Vfs*48, and IVS12+1G>A were also detected. Genetic drift and founder effect may have also played a role in the mutation spectrum we observed.
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Affiliation(s)
- Eduardo Vieira Neto
- Gerência de Monitoramento AssistencialAgência Nacional de Saúde SuplementarRio de JaneiroBrazil
- Serviço de Genética MédicaInstituto de Puericultura e Pediatria Martagão GesteiraUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
| | - Francisco Laranjeira
- Centro de Genética Médica Doutor Jacinto MagalhãesUnidade de Bioquímica GenéticaPortoPortugal
| | - Dulce Quelhas
- Centro de Genética Médica Doutor Jacinto MagalhãesUnidade de Bioquímica GenéticaPortoPortugal
| | - Isaura Ribeiro
- Centro de Genética Médica Doutor Jacinto MagalhãesUnidade de Bioquímica GenéticaPortoPortugal
| | - Alexandre Seabra
- Centro de Genética Médica Doutor Jacinto MagalhãesUnidade de Bioquímica GenéticaPortoPortugal
| | - Nicole Mineiro
- Centro de Genética Médica Doutor Jacinto MagalhãesUnidade de Bioquímica GenéticaPortoPortugal
| | - Lilian d. M. Carvalho
- Serviço de MetabologiaInstituto de Diabetes e Endocrinologia Luiz CapriglioneRio de JaneiroBrazil
| | - Lúcia Lacerda
- Centro de Genética Médica Doutor Jacinto MagalhãesUnidade de Bioquímica GenéticaPortoPortugal
| | - Márcia G. Ribeiro
- Serviço de Genética MédicaInstituto de Puericultura e Pediatria Martagão GesteiraUniversidade Federal do Rio de JaneiroRio de JaneiroBrazil
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16
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Zhang Z, Gao JJ, Feng Y, Zhu LL, Yan H, Shi XF, Chang AM, Shi Y, Wang P. Mutational spectrum of the phenylalanine hydroxylase gene in patients with phenylketonuria in the central region of China. Scand J Clin Lab Invest 2018; 78:211-218. [PMID: 29390883 DOI: 10.1080/00365513.2018.1434898] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 01/23/2018] [Accepted: 01/28/2018] [Indexed: 01/15/2023]
Abstract
Phenylketonuria (PKU, OMIM 261600) caused by phenylalanine hydroxylase (PAH) deficiency is an autosomal recessive disease that is characterized by abnormalities of phenylalanine metabolism. In this study, a total of 77 patients, originating from the central region of China and who were diagnosed with PAH deficiency at the third affiliated hospital of Zhengzhou University, were enrolled in this study. The 13 exons and 12 flanking introns of the PAH gene were analyzed by Sanger sequencing and next generation sequencing. The sequencing data were aligned to the hg19, PAHvdb and HGMD databases to characterize the genotypes of PKU patients, and genotype-phenotype correlations and BH4 responsiveness predictions were performed using BIOPKUdb. In total, 149 alleles were characterized among the 154 PKU alleles. These mutations were located in exons 2-13, and intron 12 of the PAH gene, with a relative frequency of ≥5%, for EX6-96A>G, p.R241C, p.R243Q, p.V399V and p.R53H. Additionally, a novel variant, p.D84G, was identified. The genotype correlated with clinical symptoms in 33.3-100% of the cases, depending on the disease severity, and BH4 responsiveness predictions show that only five patients with MHP-PKU and one patient with Mild-PKU were predicted to be BH4 responsive. In conclusion, we have characterized the mutational spectrum of PAH in the central region of China and have identified a novel mutation. The hotspot mutation information might be useful for screening, diagnosis and treatment of PKU.
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Affiliation(s)
- Zhan Zhang
- a The Third Affiliated Hospital of Zhengzhou University , Zhengzhou , China
- b Shangqiu Medical College , Shangqiu , China
| | - Jun-Jun Gao
- a The Third Affiliated Hospital of Zhengzhou University , Zhengzhou , China
| | - Yang Feng
- a The Third Affiliated Hospital of Zhengzhou University , Zhengzhou , China
| | - Lin-Lin Zhu
- c School of Laboratory Medicine , Xinxiang Medical University , Xinxiang , China
| | - Huan Yan
- a The Third Affiliated Hospital of Zhengzhou University , Zhengzhou , China
| | - Xu-Feng Shi
- d Department of Obstetrics , Henan Province People's Hospital , Zhengzhou , China
| | - Ai-Min Chang
- a The Third Affiliated Hospital of Zhengzhou University , Zhengzhou , China
| | - Ying Shi
- a The Third Affiliated Hospital of Zhengzhou University , Zhengzhou , China
| | - Ping Wang
- a The Third Affiliated Hospital of Zhengzhou University , Zhengzhou , China
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17
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Liu X, Zhang C, Liu K, Wang H, Lu C, Li H, Hua K, Zhu J, Hui W, Cui Y, Zhang X. Multiple SNPs Detection Based on Lateral Flow Assay for Phenylketonuria Diagnostic. Anal Chem 2018; 90:3430-3436. [PMID: 29451781 DOI: 10.1021/acs.analchem.7b05113] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are closely related to genetic diseases, but current SNP detection methods, such as DNA microarrays that include tedious procedures and expensive, sophisticated instruments, are unable to perform rapid SNPs detection in clinical practice, especially for those multiple SNPs related to genetic diseases. In this study, we report a sensitive, low cost, and easy-to-use point-of-care testing (POCT) system formed by combining amplification refractory mutation system (ARMS) polymerase chain reaction with gold magnetic nanoparticles (GMNPs) and lateral flow assay (LFA) noted as the ARMS-LFA system, which allow us to use a uniform condition for multiple SNPs detection simultaneously. The genotyping results can be explained by a magnetic reader automatically or through visual interpretation according to the captured GMNPs probes on the test and control lines of the LFA device. The high sensitivity (the detection limit of 0.04 pg/μL with plasmid) and specificity of this testing system were found through genotyping seven pathogenic SNPs in phenylalanine hydroxylase gene ( PAH, the etiological factor of phenylketonuria). This system can also be applied in DNA quantification with a linear range from 0.02 to 2 pg/μL of plasmid. Furthermore, this ARMS-LFA system was applied to clinical trials for screening the seven pathogenic SNPs in PAH of 23 families including 69 individuals. The concordance rate of the genotyping results detected by the ARMS-LFA system was up to 97.8% compared with the DNA sequencing results. This method is a very promising POCT in the detection of multiple SNPs caused by genetic diseases.
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Affiliation(s)
- Xiaonan Liu
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China
| | - Chao Zhang
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China
| | - Kewu Liu
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China
| | - Han Wang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100005 , China
| | - Chaoxia Lu
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100005 , China
| | - Hang Li
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China
| | - Kai Hua
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China.,National Engineering Research Center for Miniaturized Detection System , Xi'an , Shaanxi 710069 , China
| | - Juanli Zhu
- Shaanxi Provincial Engineering Research Center for Nano-Biomedical Detection , Xi'an , Shaanxi 710077 , China
| | - Wenli Hui
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China.,National Engineering Research Center for Miniaturized Detection System , Xi'an , Shaanxi 710069 , China
| | - Yali Cui
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China.,National Engineering Research Center for Miniaturized Detection System , Xi'an , Shaanxi 710069 , China.,Shaanxi Provincial Engineering Research Center for Nano-Biomedical Detection , Xi'an , Shaanxi 710077 , China
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100005 , China
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18
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Wang L, Wang X, He B, Cai N, Li W, Lou C, Xin S, Wu Q, Yu W, Qiang R. Mutation analysis of the phenylalanine hydroxylase gene and prenatal diagnosis of phenylketonuria in Shaanxi, China. J Pediatr Endocrinol Metab 2017; 30:1305-1310. [PMID: 29176022 DOI: 10.1515/jpem-2016-0448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 10/02/2017] [Indexed: 01/07/2023]
Abstract
BACKGROUND This study aims to investigate the spectrum and frequency of phenylalanine hydroxylase (PAH) gene mutations and the power to prenatally diagnose phenylketonuria (PKU) patients in Shaanxi, China. METHODS Polymerase chain reaction (PCR) and DNA sequencing analyses were performed to examine the PAH gene in 33 PKU patients and seven amniotic fluid samples. Thirty-four pathogenic variants were indicated in all 63 alleles, in which two probands carried three variants. RESULTS Pedigree analysis suggested that the [c.158G>A([p.R53H)][IVS7+2T>A] mutation was located at the same chromatid. However, there was a controversial viewpoint that thought the c.158G>A(p.R53H) variant was a polymorphism in the Chinese. We also found one novel indel mutation and identified the c.59_60delAGinsCC mutation of the PAH gene for the very first time. The spectrum of the PAH mutations in Shaanxi Province were similar to that among China's population. Based on the results of PAH gene analysis, we further performed prenatal genetic diagnoses for seven PKU families. All foetuses were definitively diagnosed, and their parents were provided with genetic counselling. CONCLUSIONS PAH gene analysis is a crucial method for PKU diagnosis and prenatal genetic prognosis, even though many uncommon mutations would affect the analysis and diagnosis of genetic abnormalities.
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19
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Choi R, Lee J, Park HD, Park JE, Kim YH, Ki CS, Lee SY, Song J, Kim JW, Lee DH. Reassessing the significance of the PAH c.158G>A (p.Arg53His) variant in patients with hyperphenylalaninemia. J Pediatr Endocrinol Metab 2017; 30:1211-1218. [PMID: 29032371 DOI: 10.1515/jpem-2017-0158] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 08/21/2017] [Indexed: 11/15/2022]
Abstract
BACKGROUND The accurate interpretation of sequence variation is critical for successful molecular diagnoses. It is also fundamental to the accurate diagnosis and treatment of phenylketonuria (PKU). This study aims to evaluate the significance of the c.158G>A (p.Arg53His) variant in the PAH gene, which was previously reported to be a pathogenic mutation that results in decreased phenylalanine hydroxylase enzyme activity in hyperphenylalaninemia (HPA) patients. METHODS Seven unrelated Korean patients with HPA genotyped with the c.158G>A variant were included in this study. The variant c.158G>A was classified by the standards and guidelines for the interpretation of sequence variants by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. RESULTS By both directly collecting genetic data and comprehensively reviewing the existing literature, we found that this variant is more appropriately classified as "Likely benign" rather than pathogenic. The allele's frequency is 2.57% in the general Korean population, which was greater than expected for phenylketonuria. This variant was observed to be homozygous in healthy subjects and was also observed in cis with other pathogenic variants. It is common in East Asian populations (especially in Koreans) compared to Western populations. There is a possibility that it causes decreased enzyme activity without leading to the full pathology of phenylketonuria. CONCLUSIONS This study expands our understanding of the consequences of variation in PAH and its relationship to HPA.
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20
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Jeannesson-Thivisol E, Feillet F, Chéry C, Perrin P, Battaglia-Hsu SF, Herbeth B, Cano A, Barth M, Fouilhoux A, Mention K, Labarthe F, Arnoux JB, Maillot F, Lenaerts C, Dumesnil C, Wagner K, Terral D, Broué P, de Parscau L, Gay C, Kuster A, Bédu A, Besson G, Lamireau D, Odent S, Masurel A, Guéant JL, Namour F. Genotype-phenotype associations in French patients with phenylketonuria and importance of genotype for full assessment of tetrahydrobiopterin responsiveness. Orphanet J Rare Dis 2015; 10:158. [PMID: 26666653 PMCID: PMC5024853 DOI: 10.1186/s13023-015-0375-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 12/08/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mutations in Phenylalanine Hydroxylase (PAH) gene cause phenylketonuria. Sapropterin (BH4), the enzyme cofactor, is an important therapeutical strategy in phenylketonuria. However, PAH is a highly polymorphic gene and it is difficult to identify BH4-responsive genotypes. We seek here to improve prediction of BH4-responsiveness through comparison of genotypes, BH4-loading test, predictions of responsiveness according to the literature and types and locations of mutations. METHODS A total of 364 French patients among which, 9 % had mild hyperphenylalaninemia, 17.7 % mild phenylketonuria and 73.1 % classical phenylketonuria, benefited from a 24-hour BH4-loading test and had the PAH gene sequenced and analyzed by Multiplex Ligation Probe Amplification. RESULTS Overall, 31.6 % of patients were BH4-responsive. The number of different mutations found was 127, including 26 new mutations. The mutations c.434A > T, c.500A > T, c.529G > C, c.1045 T > G and c.1196 T > C were newly classified as being BH4-responsive. We identified 261 genotypes, among which 46 were newly recognized as being BH4-responsive. Even though patients carry 2 responsive alleles, BH4-responsiveness cannot be predicted with certainty unless they present mild hyperphenylalaninemia. BH4-responsiveness cannot be predicted in patients carrying one responsive mutation only. In general, the milder the phenotype is, the stronger the BH4-response is. Almost exclusively missense mutations, particularly in exons 12, 11 and 8, are associated with BH4-responsiveness and any other type of mutation predicts a negative response. CONCLUSIONS This study is the first of its kind, in a French population, to identify the phenotype associated with several combinations of PAH mutations. As others, it highlights the necessity of performing simultaneously BH4 loading test and molecular analysis in monitoring phenylketonuria patients.
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Affiliation(s)
- Elise Jeannesson-Thivisol
- Reference Center for Inherited Metabolic Diseases, University Hospital of Nancy, 9 ave Forêt de Haye, BP 184, 54511, Vandoeuvre-lès-Nancy, France
- INSERM U954, Department of Nutrition-Genetics-Environmental Risk Exposure, University of Lorraine, 9 ave Forêt de Haye, BP 184, 54511, Vandoeuvre-lès-Nancy, France
| | - François Feillet
- Reference Center for Inherited Metabolic Diseases, University Hospital of Nancy, 9 ave Forêt de Haye, BP 184, 54511, Vandoeuvre-lès-Nancy, France
- INSERM U954, Department of Nutrition-Genetics-Environmental Risk Exposure, University of Lorraine, 9 ave Forêt de Haye, BP 184, 54511, Vandoeuvre-lès-Nancy, France
| | - Céline Chéry
- Reference Center for Inherited Metabolic Diseases, University Hospital of Nancy, 9 ave Forêt de Haye, BP 184, 54511, Vandoeuvre-lès-Nancy, France
- INSERM U954, Department of Nutrition-Genetics-Environmental Risk Exposure, University of Lorraine, 9 ave Forêt de Haye, BP 184, 54511, Vandoeuvre-lès-Nancy, France
| | - Pascal Perrin
- Reference Center for Inherited Metabolic Diseases, University Hospital of Nancy, 9 ave Forêt de Haye, BP 184, 54511, Vandoeuvre-lès-Nancy, France
- INSERM U954, Department of Nutrition-Genetics-Environmental Risk Exposure, University of Lorraine, 9 ave Forêt de Haye, BP 184, 54511, Vandoeuvre-lès-Nancy, France
| | - Shyue-Fang Battaglia-Hsu
- Reference Center for Inherited Metabolic Diseases, University Hospital of Nancy, 9 ave Forêt de Haye, BP 184, 54511, Vandoeuvre-lès-Nancy, France
- INSERM U954, Department of Nutrition-Genetics-Environmental Risk Exposure, University of Lorraine, 9 ave Forêt de Haye, BP 184, 54511, Vandoeuvre-lès-Nancy, France
| | - Bernard Herbeth
- Reference Center for Inherited Metabolic Diseases, University Hospital of Nancy, 9 ave Forêt de Haye, BP 184, 54511, Vandoeuvre-lès-Nancy, France
- INSERM U954, Department of Nutrition-Genetics-Environmental Risk Exposure, University of Lorraine, 9 ave Forêt de Haye, BP 184, 54511, Vandoeuvre-lès-Nancy, France
| | - Aline Cano
- Reference Center for Inherited Metabolic Diseases, Timone Hospital, Marseille, France
| | - Magalie Barth
- Department of Biochemistry and Genetics, Angers University Hospital, Angers, France
| | - Alain Fouilhoux
- Reference Center for Inherited Metabolic Diseases, Hospices Civils de Lyon, Bron, France
| | - Karine Mention
- Reference Center for Inherited Metabolic Diseases, Jeanne de Flandres Hospital, Lille, France
| | - François Labarthe
- Department of Pediatric Medicine, Clocheville Hospital, Tours, France
| | - Jean-Baptiste Arnoux
- Reference Center for Inherited Metabolic Diseases, Necker-Enfants Malades Hospital, Paris, France
| | - François Maillot
- Department of Internal Medicine, Tours University Hospital, Tours, France
| | | | - Cécile Dumesnil
- Pediatric Hematology and Oncology, Rouen University-Hospital, Rouen, France
| | - Kathy Wagner
- Department of Pediatrics, Lenval Hospital, Nice, France
| | - Daniel Terral
- Department of Pediatrics, Hotel-Dieu Hospital, Clermont-Ferrand, France
| | - Pierre Broué
- Department of Pediatric Hepatology and Metabolic Diseases, Children Hospital, Toulouse, France
| | | | - Claire Gay
- Department of Pediatrics, Saint-Etienne University-Hospital, Saint-Etienne, France
| | - Alice Kuster
- Pediatric Department, Nantes University Hospital, Nantes, France
| | - Antoine Bédu
- Neonatology Department, Mère-Enfant Hospital, Limoges, France
| | - Gérard Besson
- Department of Neurology, University Hospital of Grenoble, Grenoble, France
| | - Delphine Lamireau
- Department of Pediatrics, Pellegrin-Enfants Hospital, Bordeaux, France
| | - Sylvie Odent
- Department of Clinical Genetics, Rennes University Hospital, Rennes, France
| | - Alice Masurel
- Department of Medical Genetics, Dijon University-Hospital, Dijon, France
| | - Jean-Louis Guéant
- Reference Center for Inherited Metabolic Diseases, University Hospital of Nancy, 9 ave Forêt de Haye, BP 184, 54511, Vandoeuvre-lès-Nancy, France
- INSERM U954, Department of Nutrition-Genetics-Environmental Risk Exposure, University of Lorraine, 9 ave Forêt de Haye, BP 184, 54511, Vandoeuvre-lès-Nancy, France
| | - Fares Namour
- Reference Center for Inherited Metabolic Diseases, University Hospital of Nancy, 9 ave Forêt de Haye, BP 184, 54511, Vandoeuvre-lès-Nancy, France.
- INSERM U954, Department of Nutrition-Genetics-Environmental Risk Exposure, University of Lorraine, 9 ave Forêt de Haye, BP 184, 54511, Vandoeuvre-lès-Nancy, France.
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21
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Tao J, Li N, Jia H, Liu Z, Li X, Song J, Deng Y, Jin X, Zhu J. Correlation between genotype and the tetrahydrobiopterin-responsive phenotype in Chinese patients with phenylketonuria. Pediatr Res 2015; 78:691-9. [PMID: 26322415 PMCID: PMC4700046 DOI: 10.1038/pr.2015.167] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 06/17/2015] [Indexed: 01/30/2023]
Abstract
BACKGROUND A growing body of research has suggested that tetrahydrobiopterin (BH4) responsive phenotype can be predicted by the phenylalanine hydroxylase (PAH) genotype in patients with phenylketonuria (PKU), but data concerning the association between genotype and BH4 responsiveness are scarce in China. METHODS A total of 165 PKU patients from China who had undergone a 24-h loading test with BH4 administration were recruited. Genotyping was performed by the next-generation sequencing (NGS) technique. Using the predicted residual PAH activity, we analyzed the association between genotype and BH4-responsiveness. RESULTS Among the 165 patients, 40 patients (24.24%) responded to BH4. A total of 74 distinct mutations were observed, including 13 novel mutations. The mutation p.R241C was most frequently associated with response. Two known mutations (p.A322T and p.Q419R) and two novel mutations (p.L98V and IVS3-2A>T) were first reported as responsive to BH4. Residual PAH activity of at least 12.5% was needed for responsive genotypes. CONCLUSION Genotype-based predictions of BH4-responsiveness are only for selecting potential responders. Accordingly, it is necessary to test potential responders with a long-term BH4 challenge.
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Affiliation(s)
- Jing Tao
- National Centre for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sichuan, China
- West China School of Public Health, Sichuan University, Sichuan, China
| | - Nana Li
- National Centre for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sichuan, China
- Laboratory of Molecular Epidemiology for Birth Defects, West China Second University Hospital, Sichuan University, Sichuan, China
| | - Haitao Jia
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Zhen Liu
- National Centre for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sichuan, China
- Laboratory of Molecular Epidemiology for Birth Defects, West China Second University Hospital, Sichuan University, Sichuan, China
| | - Xiaohong Li
- National Centre for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sichuan, China
- Laboratory of Molecular Epidemiology for Birth Defects, West China Second University Hospital, Sichuan University, Sichuan, China
| | | | - Ying Deng
- National Centre for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sichuan, China
- Laboratory of Molecular Epidemiology for Birth Defects, West China Second University Hospital, Sichuan University, Sichuan, China
| | - Xi Jin
- National Centre for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sichuan, China
- Laboratory of Molecular Epidemiology for Birth Defects, West China Second University Hospital, Sichuan University, Sichuan, China
| | - Jun Zhu
- National Centre for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sichuan, China
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22
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Li N, Jia H, Liu Z, Tao J, Chen S, Li X, Deng Y, Jin X, Song J, Zhang L, Liang Y, Wang W, Zhu J. Molecular characterisation of phenylketonuria in a Chinese mainland population using next-generation sequencing. Sci Rep 2015; 5:15769. [PMID: 26503515 PMCID: PMC4621502 DOI: 10.1038/srep15769] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 10/01/2015] [Indexed: 11/28/2022] Open
Abstract
Phenylketonuria (PKU) is an inherited autosomal recessive disorder of phenylalanine metabolism, mainly caused by a deficiency of phenylalanine hydroxylase (PAH). The incidence of various PAH mutations differs among race and ethnicity. Here we report a spectrum of PAH mutations complied from 796 PKU patients from mainland China. The all 13 exons and adjacent intronic regions of the PAH gene were determined by next-generation sequencing. We identified 194 different mutations, of which 41 are not reported before. Several mutations reoccurred with high frequency including p.R243Q, p.EX6-96A > G, p.V399V, p.R241C, p.R111*, p.Y356*, p.R413P, and IVS4-1G > A. 76.33% of mutations were localized in exons 3, 6, 7, 11, 12. We further compared the frequency of each mutation between populations in northern and southern China, and found significant differences in 19 mutations. Furthermore, we identified 101 mutations that are not reported before in Chinese population, our study thus broadens the mutational spectrum of Chinese PKU patients. Additionally, 41 novel mutations will expand and improve PAH mutation database. Finally, our study offers proof that NGS is effective, reduces screening times and costs, and facilitates the provision of appropriate genetic counseling for PKU patients.
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Affiliation(s)
- Nana Li
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sec. 3 No. 20, South RenMin Road, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Sec. 3 No. 20, South RenMin Road, Chengdu, Sichuan, China
| | - Haitao Jia
- BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong China
| | - Zhen Liu
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sec. 3 No. 20, South RenMin Road, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Sec. 3 No. 20, South RenMin Road, Chengdu, Sichuan, China
| | - Jing Tao
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sec. 3 No. 20, South RenMin Road, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Sec. 3 No. 20, South RenMin Road, Chengdu, Sichuan, China
| | - Song Chen
- BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong China
| | - Xiaohong Li
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sec. 3 No. 20, South RenMin Road, Chengdu, Sichuan, China.,Laboratory of Molecular Epidemiology for birth defect, West China Institute of Women and Children's Health, Sichuan University, Chengdu, China
| | - Ying Deng
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sec. 3 No. 20, South RenMin Road, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Sec. 3 No. 20, South RenMin Road, Chengdu, Sichuan, China
| | - Xi Jin
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sec. 3 No. 20, South RenMin Road, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Sec. 3 No. 20, South RenMin Road, Chengdu, Sichuan, China
| | - Jiaping Song
- BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong China
| | - Liangtao Zhang
- BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong China
| | - Yu Liang
- BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong China
| | - Wei Wang
- BGI-Shenzhen, Building No. 11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong China
| | - Jun Zhu
- National Center for Birth Defect Monitoring, West China Second University Hospital, Sichuan University, Sec. 3 No. 20, South RenMin Road, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, West China Second University Hospital, Sichuan University, Sec. 3 No. 20, South RenMin Road, Chengdu, Sichuan, China.,Laboratory of Molecular Epidemiology for birth defect, West China Institute of Women and Children's Health, Sichuan University, Chengdu, China
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23
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Trunzo R, Santacroce R, D'Andrea G, Longo V, De Girolamo G, Dimatteo C, Leccese A, Bafunno V, Lillo V, Papadia F, Margaglione M. Phenylalanine hydroxylase deficiency in south Italy: Genotype-phenotype correlations, identification of a novel mutant PAH allele and prediction of BH4 responsiveness. Clin Chim Acta 2015; 450:51-5. [PMID: 26210745 DOI: 10.1016/j.cca.2015.07.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/13/2015] [Accepted: 07/14/2015] [Indexed: 10/23/2022]
Abstract
We investigated the mutation spectrum of the phenylalanine hydroxylase gene (PAH) in a cohort of patients from 33 Italian PKU families. Mutational screening of the known coding region, including conventional intron splice sites, was performed by direct sequencing of the patients' genomic DNA. Thirty-three different disease causing mutations were identified in our patient group, including 19 missense, 6 splicing, 3 nonsense, 5 deletions, with a detection rate of 100%. The most prevalent mutation was the IVS10-11G>A, accounting for 12.1% of PKU alleles studied. Other frequent mutations were: p.R261Q (9.1%), p.P281L (7.6%), and p.R408W (6.1%). We also identified one novel missense mutation, p.H290Q. A spectrum of 31 different genotypes was observed and a genotype based predictions of BH4-responsiveness were assessed. Among all genotypes, 13 were predicted to be BH4-responsive represented by thirteen PKU families. In addition, genotype-phenotype correlations were performed. This study reveals the importance of a full genotyping of PKU patients and the prediction of BH4-responsiveness, not only because of the definitive diagnosis and prediction of the optimal diet, but also to point out those patients that could benefit from new therapeutic approach. They may potentially benefit from BH4 therapy which, combined with a less strict diet, or eventually in special cases as monotherapy, may contribute to reduce nutritional deficiencies and minimize neurological and psychological dysfunctions.
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Affiliation(s)
- Roberta Trunzo
- Genetica Medica, Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi di Foggia, Italy.
| | - Rosa Santacroce
- Genetica Medica, Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi di Foggia, Italy
| | - Giovanna D'Andrea
- Genetica Medica, Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi di Foggia, Italy
| | - Vittoria Longo
- Genetica Medica, Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi di Foggia, Italy
| | - Giuseppe De Girolamo
- Genetica Medica, Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi di Foggia, Italy
| | - Claudia Dimatteo
- Genetica Medica, Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi di Foggia, Italy
| | - Angelica Leccese
- Genetica Medica, Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi di Foggia, Italy
| | - Valeria Bafunno
- Genetica Medica, Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi di Foggia, Italy
| | | | | | - Maurizio Margaglione
- Genetica Medica, Dipartimento di Medicina Clinica e Sperimentale, Università degli Studi di Foggia, Italy
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24
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Chen YF, Jia HT, Chen ZH, Song JP, Liang Y, Pei JJ, Wu ZJ, Wang J, Qiu YL, Liu G, Sun DM, Jiang XY. Mutational spectrum of phenylketonuria in Jiangsu province. Eur J Pediatr 2015; 174:1333-8. [PMID: 25894915 DOI: 10.1007/s00431-015-2539-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 04/01/2015] [Accepted: 04/06/2015] [Indexed: 12/22/2022]
Abstract
UNLABELLED Phenylketonuria (PKU) is caused by variants in the phenylalanine hydroxylase (PAH) gene. We systematically investigated all 13 exons of the PAH gene and their flanking introns in 31 unrelated patients and their parents using next-generation sequencing (NGS). A total of 33 different variants were identified in 58 of 62 mutant PAH alleles. The prevalent variants with a relative frequency of 5 % or more were c.721C > T, c.1068C > A, c.611A > G, c.1197A > T, c.728G > A, c.331C > T, and c.442-1G > A. One novel variant was identified in this study-c.699C > G. We studied genotype-phenotype correlations using the Guldberg arbitrary value (AV) system, which revealed a consistency rate of 38 % (8/21) among the 21 predicted phenotypes. The genotype-based prediction of BH4 responsiveness was also evaluated, and 14 patients (45.2 %) were predicted to be BH4 responsive. CONCLUSION This study presents the spectrum of PAH variants in Jiangsu province. The information obtained from the genotype-based prediction of BH4 responsiveness might be used for the rational selection of candidates for BH4 testing. WHAT IS KNOWN • Phenylketonuria (PKU) is caused by variants in the phenylalanine hydroxylase (PAH) gene. • The spectrum of PAH variants in different Chinese populations has been reported. What is new: • This is the first report on the spectrum of PAH variants in Jiangsu province. • This study identified one novel PAH variant-c.699C>G-and and tries to show a genotype-phenotype relationship also regarding BH4-responsiveness.
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Affiliation(s)
- Ya-fen Chen
- Department of Children Health Care, Wuxi Maternal and Child Health Hospital, No.48 Huaishu Alley, Wuxi, Jiangsu Province, China.
| | - Hai-tao Jia
- Beijing Genomics Institute at Shenzhen, Building No.11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong, China.
| | - Zhong-hai Chen
- Beijing Genomics Institute at Shenzhen, Building No.11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong, China.
| | - Jia-ping Song
- Beijing Genomics Institute at Shenzhen, Building No.11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong, China.
| | - Yu Liang
- Beijing Genomics Institute at Shenzhen, Building No.11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong, China.
| | - Jing-jing Pei
- Department of Children Health Care, Wuxi Maternal and Child Health Hospital, No.48 Huaishu Alley, Wuxi, Jiangsu Province, China.
| | - Zhi-jun Wu
- Department of Children Health Care, Wuxi Maternal and Child Health Hospital, No.48 Huaishu Alley, Wuxi, Jiangsu Province, China.
| | - Jing Wang
- Department of Children Health Care, Suqian Maternal and Child Health Hospital, No. 9 Ping-An Road, Suqian, Jiangsu Province, China.
| | - Ya-li Qiu
- Department of Children Health Care, Suqian Maternal and Child Health Hospital, No. 9 Ping-An Road, Suqian, Jiangsu Province, China.
| | - Gang Liu
- Beijing Genomics Institute at Shenzhen, Building No.11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong, China.
| | - Dong-mei Sun
- Beijing Genomics Institute at Shenzhen, Building No.11, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong, China.
| | - Xin-ye Jiang
- Department of Children Health Care, Wuxi Maternal and Child Health Hospital, No.48 Huaishu Alley, Wuxi, Jiangsu Province, China.
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25
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Biglari A, Saffari F, Rashvand Z, Alizadeh S, Najafipour R, Sahmani M. Mutations of the phenylalanine hydroxylase gene in Iranian patients with phenylketonuria. SPRINGERPLUS 2015; 4:542. [PMID: 26413448 PMCID: PMC4579200 DOI: 10.1186/s40064-015-1309-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/04/2015] [Indexed: 11/30/2022]
Abstract
Phenylketonuria (PKU) is an autosomal recessive disease which results from mutations in the phenylalanine hydroxylase (PAH) gene. The aim of this study was the identification of sixteen different mutations in Iranian patients with hyperphenylalaninemia. The mutations were detected during the characterization of PAH genotypes of 39 PKU patients from Qazvin and Zanjan provinces of Iran. PAH mutations have been analyzed by PCR and direct sequencing of PCR products of the promoter region and all 13 exons of PAH gene, including the splicing sites. A mutation detection rate of 74.3 % was realized. Two mutations were found at high frequencies: R176X (10.25 %) and p.P281L (10.25 %). The frequencies of the other mutations were: IVS2+5G>A (2.56 %), IVS2+5G>C (2.56 %), p.L48S (2.56 %), p.R243Q (2.56 %), p.R252Q (5.12 %), p.R261Q (7.69 %), p.R261X (5.12 %), p.E280K (2.56 %), p.I283N (2.56 %), IVS9+5G>A (2.56 %), IVS9+1G>A (1.28 %), IVS11+1G>C (1.28 %), p.C357R (1.28 %), c.632delC (2.56 %). The present results confirm the high heterogeneity of the PAH locus and contribute to information about the distribution and frequency of PKU mutations in the Iranian population.
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Affiliation(s)
- Alireza Biglari
- Department of Molecular Medicine and Genetics, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Fatemeh Saffari
- Department of Pediatrics, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Zahra Rashvand
- Faculty of Medicine, The Cellular and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Safarali Alizadeh
- Faculty of Medicine, The Cellular and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Reza Najafipour
- Department of Clinical Biochemistry and Genetics, Faculty of Medicine, Cellular and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
| | - Mehdi Sahmani
- Department of Clinical Biochemistry and Genetics, Faculty of Medicine, Cellular and Molecular Research Center, Qazvin University of Medical Sciences, Qazvin, Iran
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26
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Réblová K, Kulhánek P, Fajkusová L. Computational study of missense mutations in phenylalanine hydroxylase. J Mol Model 2015; 21:70. [PMID: 25750018 DOI: 10.1007/s00894-015-2620-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 02/15/2015] [Indexed: 10/23/2022]
Abstract
Hyperphenylalaninemia (HPA) is one of the most common metabolic disorders. HPA, which is transmitted by an autosomal recessive mode of inheritance, is caused by mutations of the phenylalanine hydroxylase gene. Most mutations are missense and lead to reduced protein stability and/or impaired catalytic function. The impact of such mutations varies, ranging from classical phenylketonuria (PKU), mild PKU, to non-PKU HPA phenotypes. Despite the fact that HPA is a monogenic disease, clinical data show that one PKU genotype can be associated with more in vivo phenotypes, which indicates the role of other (still unknown) factors. To better understand the phenotype-genotype relationships, we analyzed computationally the impact of missense mutations in homozygotes stored in the BIOPKU database. A total of 34 selected homozygous genotypes was divided into two main groups according to their phenotypes: (A) genotypes leading to non-PKU HPA or combined phenotype non-PKU HPA/mild PKU and (B) genotypes leading to classical PKU, mild PKU or combined phenotype mild PKU/classical PKU. Combining in silico analysis and molecular dynamics simulations (in total 3 μs) we described the structural impact of the mutations, which allowed us to separate 32 out of 34 mutations between groups A and B. Testing the simulation conditions revealed that the outcome of mutant simulations can be modulated by the ionic strength. We also employed programs SNPs3D, Polyphen-2, and SIFT but based on the predictions performed we were not able to discriminate mutations with mild and severe PKU phenotypes.
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Affiliation(s)
- Kamila Réblová
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic,
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27
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Cao YY, Qu YJ, Song F, Zhang T, Bai JL, Jin YW, Wang H. Fast clinical molecular diagnosis of hyperphenylalaninemia using next-generation sequencing-based on a custom AmpliSeq™ panel and Ion Torrent PGM sequencing. Mol Genet Metab 2014; 113:261-6. [PMID: 25456745 DOI: 10.1016/j.ymgme.2014.10.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 10/05/2014] [Accepted: 10/05/2014] [Indexed: 12/15/2022]
Abstract
Hyperphenylalaninemia (HPA) can be classified into phenylketonuria (PKU) and tetrahydrobiopterin deficiency (BH4D), according to the defect of enzyme activity, both of which vary substantially in severity, treatment, and prognosis of the disease. To set up a fast and comprehensive assay in order to achieve early etiological diagnosis and differential diagnosis for children with HPA, we designed a custom AmpliSeq™ panel for the sequencing of coding DNA sequence (CDS), flanking introns, 5' untranslated region (UTR) and 3' UTR from five HPA-causing genes (PAH, PTS, QDPR, GCH1, and PCBD1) using the Ion Torrent Personal Genome Machine (PGM) Sequencer. A standard group of 15 samples with previously known DNA sequences and a test group of 37 HPA patients with unknown mutations were used for assay validation and application, respectively. All variations were confirmed by Sanger sequencing. In the standard group, all the known mutations were detected and were consistent with the results of previous Sanger sequencing. In the test group, we identified mutations in 71 of 74 alleles, with a mutation detection rate of 95.9%. We also found a frame shift deletion p.Ile25Metfs*13 in PAH that was previously unreported. In addition, 1 of 37 in the test group was inconsistent with either the molecular diagnosis or clinical diagnosis by traditional differential methods. In conclusion, our comprehensive assay based on a custom AmpliSeq™ panel and Ion Torrent PGM sequencing has wider coverage, higher throughput, is much faster, and more efficient when compared with the traditional molecular detection method for HPA patients, which could meet the medical need for individualized diagnosis and treatment.
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Affiliation(s)
- Yan-yan Cao
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| | - Yu-jin Qu
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| | - Fang Song
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| | - Ting Zhang
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| | - Jin-li Bai
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| | - Yu-wei Jin
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| | - Hong Wang
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
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28
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Gu Y, Lu K, Yang G, Cen Z, Yu L, Lin L, Hao J, Yang Z, Peng J, Cui S, Huang J. Mutation spectrum of six genes in Chinese phenylketonuria patients obtained through next-generation sequencing. PLoS One 2014; 9:e94100. [PMID: 24705691 PMCID: PMC3976377 DOI: 10.1371/journal.pone.0094100] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2013] [Accepted: 03/11/2014] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The identification of gene variants plays an important role in the diagnosis of genetic diseases. METHODOLOGY/PRINCIPAL FINDINGS To develop a rapid method for the diagnosis of phenylketonuria (PKU) and tetrahydrobiopterin (BH4) deficiency, we designed a multiplex, PCR-based primer panel to amplify all the exons and flanking regions (50 bp average) of six PKU-associated genes (PAH, PTS, GCH1, QDPR, PCBD1 and GFRP). The Ion Torrent Personal Genome Machine (PGM) System was used to detect mutations in all the exons of these six genes. We tested 93 DNA samples from blood specimens from 35 patients and their parents (32 families) and 26 healthy adults. Using strict bioinformatic criteria, this sequencing data provided, on average, 99.14% coverage of the 39 exons at more than 70-fold mean depth of coverage. We found 23 previously documented variants in the PAH gene and six novel mutations in the PAH and PTS genes. A detailed analysis of the mutation spectrum of these patients is described in this study. CONCLUSIONS/SIGNIFICANCE These results were confirmed by Sanger sequencing. In conclusion, benchtop next-generation sequencing technology can be used to detect mutations in monogenic diseases and can detect both point mutations and indels with high sensitivity, fidelity and throughput at a lower cost than conventional methods in clinical applications.
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Affiliation(s)
- Ying Gu
- Prenatal Diagnosis Center, Maternal and Child Health Care Hospital, Lianyungang, Jiangsu, China
| | - Kangmo Lu
- Prenatal Diagnosis Center, Chengdu Women's and Children's Central Hospital, Chengdu, Sichuan, China
| | | | - Zhong Cen
- Shanghai Find Bio-Tech Co., Ltd., Shanghai, China
| | - Li Yu
- Life Technologies Company, Shanghai, China
| | - Lin Lin
- Shanghai Find Bio-Tech Co., Ltd., Shanghai, China
| | - Jing Hao
- Shanghai Find Bio-Tech Co., Ltd., Shanghai, China
| | - Zhigang Yang
- Shanghai Find Bio-Tech Co., Ltd., Shanghai, China
| | - Jiabao Peng
- Shanghai Find Bio-Tech Co., Ltd., Shanghai, China
| | - Shujian Cui
- Shanghai Find Bio-Tech Co., Ltd., Shanghai, China
| | - Jian Huang
- National Engineering Center for Biochip at Shanghai, Shanghai, China
- Shanghai-MOST Key Laboratory for Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
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Abstract
Phenylketonuria (PKU) is an inborn error of metabolism of the amino acid phenylalanine. It is an autosomal recessive disorder with a rate of incidence of 1 in 10,000 in Caucasian populations. Mutations in the phenylalanine hydroxylase (PAH) gene are the major cause of PKU, due to the loss of the catalytic activity of the enzyme product PAH. Newborn screening for PKU allows early intervention, avoiding irreparable neurological damage and intellectual disability that would arise from untreated PKU. The current primary treatment of PKU is the limitation of dietary protein intake, which in the long term may be associated with poor compliance in some cases and other health problems due to malnutrition. The only alternative therapy currently approved is the supplementation of BH4, the requisite co-factor of PAH, in the orally-available form of sapropterin dihydrochloride. This treatment is not universally available, and is only effective for a proportion (estimated 30%) of PKU patients. Research into novel therapies for PKU has taken many different approaches to address the lack of PAH activity at the core of this disorder: enzyme replacement via virus-mediated gene transfer, transplantation of donor liver and recombinant PAH protein, enzyme substitution using phenylalanine ammonia lyase (PAL) to provide an alternative pathway for the metabolism of phenylalanine, and restoration of native PAH activity using chemical chaperones and nonsense read-through agents. It is hoped that continuing efforts into these studies will translate into a significant improvement in the physical outcome, as well as quality of life, for patients with PKU.
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Affiliation(s)
- Gladys Ho
- 1 Genetic Metabolic Disorders Research Unit; 2 Disciplines of Paediatrics and Child Health and 3 Genetic Medicine, University of Sydney, Sydney, NSW, Australia ; 4 Genetic Metabolic Disorders Service, Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, NSW, Australia
| | - John Christodoulou
- 1 Genetic Metabolic Disorders Research Unit; 2 Disciplines of Paediatrics and Child Health and 3 Genetic Medicine, University of Sydney, Sydney, NSW, Australia ; 4 Genetic Metabolic Disorders Service, Western Sydney Genetics Program, Children's Hospital at Westmead, Sydney, NSW, Australia
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The mutation spectrum of the phenylalanine hydroxylase (PAH) gene and associated haplotypes reveal ethnic heterogeneity in the Taiwanese population. J Hum Genet 2014; 59:145-52. [PMID: 24401910 DOI: 10.1038/jhg.2013.136] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 11/29/2013] [Accepted: 12/05/2013] [Indexed: 02/01/2023]
Abstract
Phenylalanine hydroxylase (PAH) deficiency is responsible for most cases of phenylketonuria (PKU). In this study of the PAH mutation spectrum in the Taiwanese population, 139 alleles were identified including 34 different mutations. The V190G, Q267R and F392I mutations are first reported in this study. The most common mutations, R241C, R408Q and Ex6-96A>G, account for 23.2%, 12.0% and 9.2%, of the mutant alleles, respectively. Haplotype analysis shows that R241C and Ex6-96A>G are exclusively associated with haplotype 4.3 to suggest founder effects. On the other hand, R408Q is found on two distinct haplotypes suggesting recurrent mutations. The spectrum of PAH mutations in Taiwan shows various links to those of other Asian regions, yet remarkable differences exist. Notably, R408Q, E286K and -4173_-407del, accounting for 21% of all mutant alleles in Taiwan, are very rare or are undetected among PKU cohorts of other Asian regions to suggest local founder effects. Moreover, the low homozygosity value of 0.092 hints at a high degree of ethnic heterogeneity within the Taiwanese population. Our study of PAH mutation spectrum and the associated haplotypes is useful for subsequent study on the origin and migration pattern via Taiwan, an island at the historical crossroad of migration of ancient populations.
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Bashyam MD, Chaudhary AK, Kiran M, Nagarajaram HA, Devi RR, Ranganath P, Dalal A, Bashyam L, Gupta N, Kabra M, Muranjan M, Puri RD, Verma IC, Nampoothiri S, Kadandale JS. Splice, insertion-deletion and nonsense mutations that perturb the phenylalanine hydroxylase transcript cause phenylketonuria in India. J Cell Biochem 2013; 115:566-74. [PMID: 24130151 DOI: 10.1002/jcb.24692] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 10/10/2013] [Indexed: 01/20/2023]
Abstract
Phenylketonuria (PKU) is an autosomal recessive metabolic disorder caused by mutational inactivation of the phenylalanine hydroxylase (PAH) gene. Missense mutations are the most common PAH mutation type detected in PKU patients worldwide. We performed PAH mutation analysis in 27 suspected Indian PKU families (including 7 from our previous study) followed by structure and function analysis of specific missense and splice/insertion-deletion/nonsense mutations, respectively. Of the 27 families, disease-causing mutations were detected in 25. A total of 20 different mutations were identified of which 7 "unique" mutations accounted for 13 of 25 mutation positive families. The unique mutations detected exclusively in Indian PKU patients included three recurrent mutations detected in three families each. The 20 mutations included only 5 missense mutations in addition to 5 splice, 4 each nonsense and insertion-deletion mutations, a silent variant in coding region and a 3'UTR mutation. One deletion and two nonsense mutations were characterized to confirm significant reduction in mutant transcript levels possibly through activation of nonsense mediated decay. All missense mutations affected conserved amino acid residues and sequence and structure analysis suggested significant perturbations in the enzyme activity of respective mutant proteins. This is probably the first report of identification of a significantly low proportion of missense PAH mutations from PKU families and together with the presence of a high proportion of splice, insertion-deletion, and nonsense mutations, points to a unique PAH mutation profile in Indian PKU patients.
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Affiliation(s)
- Murali D Bashyam
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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Zhu T, Ye J, Han L, Qiu W, Zhang H, Liang L, Gu X. Variations in genotype–phenotype correlations in phenylalanine hydroxylase deficiency in Chinese Han population. Gene 2013; 529:80-7. [DOI: 10.1016/j.gene.2013.07.079] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 07/19/2013] [Accepted: 07/22/2013] [Indexed: 11/16/2022]
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33
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Couce ML, Bóveda MD, Fernández-Marmiesse A, Mirás A, Pérez B, Desviat LR, Fraga JM. Molecular epidemiology and BH4-responsiveness in patients with phenylalanine hydroxylase deficiency from Galicia region of Spain. Gene 2013; 521:100-4. [PMID: 23500595 DOI: 10.1016/j.gene.2013.03.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 02/28/2013] [Accepted: 03/01/2013] [Indexed: 11/16/2022]
Abstract
Knowledge of hyperphenylalaninemia (HPA) mutational spectrum in a population allows in many cases an accurate prediction of the phenotype and tetrahydrobiopterin (BH4) responsiveness, thus selecting an adequate treatment. In this work, we have performed the molecular characterization of 105 HPA patients from Galicia, in the northwest region of Spain, evaluating their phenotype and BH4 response. The mutational spectrum analysis showed 47 distinct mutations in 89 families, 37 of them (78.7%) corresponding to missense mutations. Six mutations account for 47.2% of all the investigated alleles, each one with a frequency ≥ 5% (IVS10-11G>A, p.R261Q, p.V388M, p.R176L, p.E280K, p.A300S). The most prevalent HPA mutations in Galicia are the common Mediterranean mutation IVS10-11G>A and p.R261Q, with frequencies of 13.8% and 10.5%, respectively. One novel mutation (p.K361Q; c.1081A>C) was also reported. Although a good genotype-phenotype correlation is observed, there is no exact correlation for some genotypes involving mutations p.R261Q, p.I65T or IVS10-11G>A. Forty seven patients were monitored for post-challenge BH4, establishing genotype-based predictions of BH4-responsiveness in all of them. All phenylketonuric patients with 2 nonresponsive mutations were unresponsive to BH4 and patients with mutations previously associated with BH4 responsiveness in the two alleles had a clear positive response to the test, with the exception of 5 patients with mutations p.R261Q, p.I65T and p.R68S. Our study supports a similar degree of heterogeneity of the HPA mutation spectrum in Galicia compared to reported data from Southern Europe. Patients carrying null mutations in both alleles showed the highest degree of concordance with the most severe phenotypes. Genotype is a good predictor of BH4 response.
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Affiliation(s)
- M L Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Department of Pediatrics, Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain.
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34
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Baturina OA, Bondar AA, Tupikin AE, Zhabin SG, Morozov IV. Analysis of phenylalanine hydroxylase gene mutations in phenylketonuria patients from Kemerovo oblast and the Sakha Republic. CYTOL GENET+ 2012. [DOI: 10.3103/s0095452712040032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Polymorphism and Sequencing Analysis of Mutations in Patients with Phenylketonuria. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2011. [DOI: 10.1016/s1872-2040(10)60486-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Okano Y, Kudo S, Nishi Y, Sakaguchi T, Aso K. Molecular characterization of phenylketonuria and tetrahydrobiopterin-responsive phenylalanine hydroxylase deficiency in Japan. J Hum Genet 2011; 56:306-12. [PMID: 21307867 DOI: 10.1038/jhg.2011.10] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Phenylketonuria (PKU) is a heterogeneous metabolic disorder caused by a deficiency in hepatic phenylalanine hydroxylase (PAH). On the basis of phenotype/genotype correlations, determination of phenylketonuric genotype is important for classification of the clinical phenotype and treatment of PKU, including tetrahydrobiopterin therapy. We characterized the genotypes of 203 Japanese patients with PKU and hyperphenylalaninemia using the following systems: (1) denaturing high-performance liquid chromatography with a GC-clamped primer; (2) direct sequencing; and, (3) multiplex ligation-dependent probe amplification. Of 406 mutant alleles, 390 (96%) were genotyped; 65 mutations were identified, including 22 new mutations. R413P, R241C, IVS4-1g>a, R111X and R243Q were prevalent mutations. Mutations prevalent in the Japanese cohort are also common in Korean and Northern Chinese populations, suggesting same origin. The spectrum of prevalent mutations was not significantly different among six Japanese districts, indicating that Japan comprises a relatively homogeneous ethnic group. We classified the mutations by clinical phenotypes and in vivo PAH activity and estimated the mutations with potential tetrahydrobiopterin (BH(4)) responsiveness. The frequency of BH(4) responsiveness based on the genotype was 29.1% in Japanese PKU patients. A catalog of PKU genotypes would be useful for predicting clinical phenotype, deciding on the subsequent treatment of PKU including BH(4) therapy, and genetic counseling in East Asia.
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Affiliation(s)
- Yoshiyuki Okano
- Department of Pediatrics, Osaka City University Graduate School of Medicine, Osaka, Japan.
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37
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Bashyam MD, Chaudhary AK, Reddy EC, Devi ARR, Savithri GR, Ratheesh R, Bashyam L, Mahesh E, Sen D, Puri R, Verma IC, Nampoothiri S, Vaidyanathan S, Chandrashekar MD, Kantheti P. Phenylalanine hydroxylase gene mutations in phenylketonuria patients from India: identification of novel mutations that affect PAH RNA. Mol Genet Metab 2010; 100:96-9. [PMID: 20188615 DOI: 10.1016/j.ymgme.2010.01.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Revised: 01/27/2010] [Accepted: 01/27/2010] [Indexed: 11/20/2022]
Abstract
Analysis of seven Indian phenylketonuria families has revealed four novel mutations in the phenylalanine hydroxylase gene; two affected consensus splice sequence and the 3' UTR, respectively, while the other two were single base insertion and deletion mutations, respectively. A novel 3' splice site mutation c.168-2A>G resulted in the activation of a cryptic 3' splice site that generated a premature termination codon leading to very low levels of the mutant transcript, probably due to activation of the nonsense-mediated decay (NMD) pathway. This is probably the first report of PKU caused by the activation of NMD.
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Affiliation(s)
- Murali D Bashyam
- Laboratory of Molecular Oncology, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.
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38
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Zhu T, Qin S, Ye J, Qiu W, Han L, Zhang Y, Gu X. Mutational spectrum of phenylketonuria in the Chinese Han population: a novel insight into the geographic distribution of the common mutations. Pediatr Res 2010; 67:280-5. [PMID: 19915519 DOI: 10.1203/pdr.0b013e3181c9fb85] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The absence of a comprehensive analysis for phenylketonuria (PKU) mutations in the Chinese Han population has resulted in continued studies during the past 18 y to elucidate the mutational spectrum in patients from virtually all Chinese regions. Our study systematically investigated 13 exons and their surrounding introns of the phenylalanine hydroxylase (PAH) gene in 212 unrelated patients using PCR and direct sequencing. A total of 79 different mutations were identified in 405 of 424 mutant PAH alleles including 15 novel ones. Eight mutations, R243Q, Ex6-96A>G, IVS4 - 1G>A, R413P, Y356X, R111X, R241C, and V399V, with a relative frequency of 3% or more, accounted for two thirds of the identified ones. The data presented in this study indicates that the total pool of mutant PAH alleles in China consisted of a small number of common mutations and a very high number of rare mutations. Moreover, by merging the findings of previous studies to generate a more composite data set for the Chinese mainland, it is shown that there are no significant differences of the common mutations between southern and northern except for R413P statistically, raising questions about the previous hypothesis that great variations on mutation frequencies exist between above regions.
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Affiliation(s)
- Tianwen Zhu
- Department of Endocrinology and Genetic Metabolism, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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39
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Daniele A, Scala I, Cardillo G, Pennino C, Ungaro C, Sibilio M, Parenti G, Esposito L, Zagari A, Andria G, Salvatore F. Functional and structural characterization of novel mutations and genotype-phenotype correlation in 51 phenylalanine hydroxylase deficient families from Southern Italy. FEBS J 2009; 276:2048-59. [DOI: 10.1111/j.1742-4658.2009.06940.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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Lee YW, Lee DH, Kim ND, Lee ST, Ahn JY, Choi TY, Lee YK, Kim SH, Kim JW, Ki CS. Mutation analysis of PAH gene and characterization of a recurrent deletion mutation in Korean patients with phenylketonuria. Exp Mol Med 2009; 40:533-40. [PMID: 18985011 DOI: 10.3858/emm.2008.40.5.533] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Phenylketonuria (PKU; MIM 261600) is an autosomal recessive metabolic disorder caused by a deficiency of phenylalanine hydroxylase (PAH; EC 1.14.16.1). Point mutations in the PAH gene are known to cause PKU in various ethnic groups, and large deletions or duplications account for up to 3% of the PAH mutations in some ethnic groups. However, a previous study could not identify approximately 14% of the mutant alleles by sequence analysis in Korean patients with PKU, which suggests that large deletions or duplication might be frequent causes of PKU in Koreans. To test this hypothesis, we performed multiplex ligation-dependent probe amplification (MLPA) for the identification of uncharacterized mutant alleles after PAH sequence analysis of 33 unrelated Korean patients with PKU. Bi-directional sequencing of the PAH exons and flanking intronic regions revealed 27 different mutations, including four novel mutations (two missense and two deletion mutations), comprising 57/66 (86%) mutant alleles. MLPA identified a large deletion that encompassed exons 5 and 6 in four patients, another large deletion that extended from exon 4 to exon 7 in one patient, and a duplication of exon 4 in one patient. Chromosomal walking characterized the deletion breakpoint of the most common large deletion that involved exons 5 and 6 (c.456_706+138del). The present study shows that the allelic frequency of exon deletion or duplication is 9% (6/66) in Korean PKU patients, which suggests that these mutations may be frequent causes of PKU in Korean subjects.
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Affiliation(s)
- Yong Wha Lee
- Department of Laboratory Medicine and Genetics, Soonchunhyang University Bucheon Hospital, Soonchunhyang Univerisity College of Medicine, Bucheon 420-767, Korea
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41
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Mutation characteristics of the PAH gene in four nationality groups in Xinjiang of China. J Genet 2008; 87:293-7. [DOI: 10.1007/s12041-008-0047-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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42
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Santos LL, Castro-Magalhães M, Fonseca CG, Starling ALP, Januário JN, Aguiar MJB, Carvalho MRS. PKU in Minas Gerais State, Brazil: mutation analysis. Ann Hum Genet 2008; 72:774-9. [PMID: 18798839 DOI: 10.1111/j.1469-1809.2008.00476.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work was undertaken in order to ascertain the PKU mutational spectrum in Minas Gerais, Brazil, the relative frequency of the mutations in the State and the origin of these mutations by haplotype determination. Minas Gerais is a trihybrid population formed by miscegenation from Europeans, Africans and Amerindians. All 13 exons of the PAH gene from 78 PKU patients were analyzed, including splicing sites and the promoter region. We identified 30 different mutations and 98% of the PAH alleles were established. A new mutation (Q267X) was identified as well. The most common mutations found were V388M (21.2), R261Q (16.0%), IVS10-11G>A (15.3%), I65T (5.8%), IVS2+5G>C (5.8%), R252W (5.1%), IVS2+5G>A (4.5%), P281L (3.8%) and L348V (3.2%). These nine mutations correspond to 80% of the PKU alleles in the state. Haplotypes were determined to characterize the origin of the PAH alleles. The majority of the mutations found, with respective haplotypes, are frequent in the Iberian Peninsula. However, there were some mutations that are rare in Europe and four previously unreported mutation-haplotype associations. I65T and Q267X were found in association with haplotype 38 and may be African in origin or the result of miscegenation in the Brazilian population.
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Affiliation(s)
- L L Santos
- Departamento de Biologia, Universidade Federal de Minas Gerais-Instituto de Ciências Biológicas, Belo Horizonte, MG, Brazil
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43
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Bercovich D, Elimelech A, Zlotogora J, Korem S, Yardeni T, Gal N, Goldstein N, Vilensky B, Segev R, Avraham S, Loewenthal R, Schwartz G, Anikster Y. Genotype-phenotype correlations analysis of mutations in the phenylalanine hydroxylase (PAH) gene. J Hum Genet 2008; 53:407-418. [PMID: 18299955 DOI: 10.1007/s10038-008-0264-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2007] [Accepted: 01/28/2008] [Indexed: 10/22/2022]
Abstract
The aims of our research were to define the genotype-phenotype correlations of mutations in the phenylalanine hydroxylase (PAH) gene that cause phenylketonuria (PKU) among the Israeli population. The mutation spectrum of the PAH gene in PKU patients in Israel is described, along with a discussion on genotype-phenotype correlations. By using polymerase chain reaction/denaturing high-performance liquid chromatography (PCR/dHPLC) and DNA sequencing, we screened all exons of the PAH gene in 180 unrelated patients with four different PKU phenotypes [classic PKU, moderate PKU, mild PKU, and mild hyperphenylalaninemia (MHP)]. In 63.2% of patient genotypes, the metabolic phenotype could be predicted, though evidence is also found for both phenotypic inconsistencies among subjects with more than one type of mutation in the PAH gene. Data analysis revealed that about 25% of patients could participate in the future in (6R)-L: -erythro-5, 6, 7, 8-tetrahydrobiopterin (BH4) treatment trials according to their mutation genotypes. This study enables us to construct a national database in Israel that will serve as a valuable tool for genetic counseling and a prognostic evaluation of future cases of PKU.
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Affiliation(s)
- Dani Bercovich
- MIGAL, Galilee Technology Center, Human Molecular Genetics and Pharmacogenetics Laboratory, Kiryat Shmona, Israel. .,Tel-Hai Academic College, Upper Galilee, Israel.
| | - Arava Elimelech
- MIGAL, Galilee Technology Center, Human Molecular Genetics and Pharmacogenetics Laboratory, Kiryat Shmona, Israel
| | - Joel Zlotogora
- Department of Genetic Community, Public Health Services, Health Ministry and Hebrew University, Jerusalem, Israel
| | - Sigal Korem
- MIGAL, Galilee Technology Center, Human Molecular Genetics and Pharmacogenetics Laboratory, Kiryat Shmona, Israel.,Tel-Hai Academic College, Upper Galilee, Israel
| | - Tal Yardeni
- MIGAL, Galilee Technology Center, Human Molecular Genetics and Pharmacogenetics Laboratory, Kiryat Shmona, Israel
| | - Nurit Gal
- Metabolic Disease Unit, Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Nurit Goldstein
- Metabolic Disease Unit, Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Bela Vilensky
- Metabolic Disease Unit, Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Roni Segev
- Metabolic Disease Unit, Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Smadar Avraham
- Metabolic Disease Unit, Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Ron Loewenthal
- Tissue Typing Unit and Safra Children Hospital, Sheba Medical Center, Tel-Hashomer, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Gerard Schwartz
- Metabolic Disease Unit, Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel
| | - Yair Anikster
- Metabolic Disease Unit, Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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44
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Zurflüh MR, Zschocke J, Lindner M, Feillet F, Chery C, Burlina A, Stevens RC, Thöny B, Blau N. Molecular genetics of tetrahydrobiopterin-responsive phenylalanine hydroxylase deficiency. Hum Mutat 2008; 29:167-75. [PMID: 17935162 DOI: 10.1002/humu.20637] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Mutations in the phenylalanine hydroxylase (PAH) gene result in phenylketonuria (PKU). Tetrahydrobiopterin (BH(4))-responsive hyperphenylalaninemia has been recently described as a variant of PAH deficiency caused by specific mutations in the PAH gene. It has been suggested that BH(4)-responsiveness may be predicted from the corresponding genotypes. Data from BH(4) loading tests indicated an incidence of BH(4)-responsiveness of >40% in the general PKU population and >80% in mild PKU patients. The current project entailed genotype analysis of 315 BH(4)-responsive patients tabulated in the BIOPKUdb database and comparison with the data from the PAHdb locus-specific knowledgebase, as well as with previously published PAH mutations for several European countries, Northern China, and South Korea. We identified 57 mutations, presenting with a substantial residual PAH activity (average approximately 47%), presumed to be associated with BH(4)-responsiveness. More than 89% of patients are found to be compound heterozygotes. The three most common mutations found in >5% of BH(4)-responsive patients are p.A403 V, p.R261Q, and p.Y414C. Using the Hardy-Weinberg formula the predicted average frequency of BH(4)-responsiveness in European populations was calculated to be 55% (range 17-79%, lowest in Baltic countries and Poland and highest in Spain), 57% in Northern China, and 55% for South Korea. The genotype-predicted prevalence of BH(4)-responsiveness was higher than prevalence data obtained from BH(4) loading tests. Inconsistent results were observed for mutations p.L48S, p.I65 T, p.R158Q, p.R261Q, and p.Y414C. Our data suggest that BH(4)-responsiveness may be more common than assumed and to some extent may be predicted or excluded from the patient's genotype.
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Affiliation(s)
- Marcel R Zurflüh
- Division of Clinical Chemistry and Biochemistry, University Children's Hospital, Zürich, Switzerland
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45
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Abstract
"Inborn errors of metabolism," first recognized 100 years ago by Garrod, were seen as transforming evidence for chemical and biological individuality. Phenylketonuria (PKU), a Mendelian autosomal recessive phenotype, was identified in 1934 by Asbjörn Fölling. It is a disease with impaired postnatal cognitive development resulting from a neurotoxic effect of hyperphenylalaninemia (HPA). Its metabolic phenotype is accountable to multifactorial origins both in nurture, where the normal nutritional experience introduces L-phenylalanine, and in nature, where mutations (>500 alleles) occur in the phenylalanine hydroxylase gene (PAH) on chromosome 12q23.2 encoding the L-phenylalanine hydroxylase enzyme (EC 1.14.16.1). The PAH enzyme converts phenylalanine to tyrosine in the presence of molecular oxygen and catalytic amounts of tetrahydrobiopterin (BH4), its nonprotein cofactor. PKU is among the first of the human genetic diseases to enter, through newborn screening, the domain of public health, and to show a treatment effect. This effect caused a paradigm shift in attitudes about genetic disease. The PKU story contains many messages, including: a framework on which to appreciate the complexity of PKU in which phenotype reflects both locus-specific and genomic components; what the human PAH gene tells us about human population genetics and evolution of modern humans; and how our interest in PKU is served by a locus-specific mutation database (http://www.pahdb.mcgill.ca; last accessed 20 March 2007). The individual Mendelian PKU phenotype has no "simple" or single explanation; every patient has her/his own complex PKU phenotype and will be treated accordingly. Knowledge about PKU reveals genomic components of both disease and health.
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Affiliation(s)
- Charles R Scriver
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
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46
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Hardelid P, Cortina-Borja M, Munro A, Jones H, Cleary M, Champion MP, Foo Y, Scriver CR, Dezateux C. The Birth Prevalence of PKU in Populations of European, South Asian and Sub-Saharan African Ancestry Living in South East England. Ann Hum Genet 2007; 72:65-71. [DOI: 10.1111/j.1469-1809.2007.00389.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Dobrowolski SF, Ellingson C, Coyne T, Grey J, Martin R, Naylor EW, Koch R, Levy HL. Mutations in the phenylalanine hydroxylase gene identified in 95 patients with phenylketonuria using novel systems of mutation scanning and specific genotyping based upon thermal melt profiles. Mol Genet Metab 2007; 91:218-27. [PMID: 17502162 DOI: 10.1016/j.ymgme.2007.03.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Accepted: 03/13/2007] [Indexed: 11/24/2022]
Abstract
Phenylketonuria (PKU, MIM 261600; EC 1.14.16.1) results from mutations in the phenylalanine hydroxylase (PAH) gene. Newborn metabolic disease screening uses blood dried on filter paper (DBS) to prospectively identify candidate newborns affected with PKU via an elevated concentration of phenylalanine. However, it is then important to confirm the specific category of PKU since classical PKU requires a stringent diet while milder categories may not require diet and a very important BH4-responsive category may be treated with the PAH cofactor 6R-tetrahydrobiopterin (BH4). Since there is a close genotype-phenotype correlation in PKU, determining the PAH genotype can be extremely important for therapy as well as prognosis. A simple and rapid method of accurately determining the PAH genotype would be a valuable addition to the diagnosis of PKU. Described herein is a means to identify variants in the PAH gene using high-resolution melt profiling, which compares the thermal denaturation profile of a patient sample to that of a control. Regions where the patient and control samples produce a common profile were not further evaluated, while those regions where the patient profile deviates from the control were assessed by DNA sequencing. Additionally described is a scheme utilizing redundant analysis with melt profile controls and a novel multiplex genotyping assay to triage deviation owing to known polymorphisms. Two mutations were identified in 93 of the 95 patients assessed and in the remaining two patients a single mutation was identified. Melt profiling provided 99% sensitivity to identify sequence variants in the PAH gene.
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de Baulny HO, Abadie V, Feillet F, de Parscau L. Management of phenylketonuria and hyperphenylalaninemia. J Nutr 2007; 137:1561S-1563S; discussion 1573S-1575S. [PMID: 17513425 DOI: 10.1093/jn/137.6.1561s] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hyperphenylalaninemia (HPA) is the most frequently inherited disorder of amino acid metabolism (prevalence 1:10,000). In France, a nationwide neonatal screening was organized in 1978 to control its efficacy and patient follow-up. Phenylketonuria (PKU) was diagnosed in 81.6% of screened patients, the remaining affected with either non-PKU HPA (17.2%) or with cofactor deficiency (1.1%). French guidelines were established to specify the minimal diagnosis procedures and optimal treatment of patients. A low-phenylalanine diet must be started within the first days of life for all newborns whose blood phenylalanine levels are above 10 mg/dL (600 micromol/L). The dietary control must keep the phenylalanine levels between 2 and 5 mg/dL (120 and 300 micromol/L) until 10 y of age. Thereafter, a progressive and controlled relaxation of the diet is allowed, keeping levels below 15 mg/dL until the end of adolescence and below 20 mg/dL (1200 micromol/L) in adulthood. A lifelong follow-up is recommended for PKU women to prevent for maternal PKU.
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Affiliation(s)
- Hélène Ogier de Baulny
- Service de Neurologie et Maladies Métaboliques, Hôpital R. Debré, Assistance Publique des Hôpitaux de Paris, 75019 Paris, France.
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Kozak L, Hrabincova E, Kintr J, Horky O, Zapletalova P, Blahakova I, Mejstrik P, Prochazkova D. Identification and characterization of large deletions in the phenylalanine hydroxylase (PAH) gene by MLPA: evidence for both homologous and non-homologous mechanisms of rearrangement. Mol Genet Metab 2006; 89:300-9. [PMID: 16931086 DOI: 10.1016/j.ymgme.2006.06.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2006] [Revised: 06/13/2006] [Accepted: 06/13/2006] [Indexed: 11/19/2022]
Abstract
Large gene deletions and duplications were analyzed in 59 unrelated phenylketonuria (PKU) patients negative for phenylalanine hydroxylase (PAH) mutations on one or both alleles from previous exon by exon analysis. Using the novel multiplex ligation-dependent probe amplification (MLPA) method, a total of 31 partial PAH deletions involving single exons were identified in 31 PKU patients. Nineteen cases exhibited deletion of exon 5, and 12 cases provided evidence for the deletion of exon 3. Subsequently, using restriction enzyme digestion and DNA sequencing, three different large deletions, EX3del4765 (12 cases), EX5del955 (2 cases) and EX5del4232ins268 (17 cases) were identified and confirmed by long-range PCR and by the analysis of aberrant transcripts. Altogether, the 31 large deletions presented account for 3% of all PAH mutant alleles investigated in Czech PKU patients. Bioinformatic analysis of three breakpoints showed that the mutation EX3del4765 had arisen through an Alu-Alu homologous recombination, whereas two other mutations-the EX5del955 and EX5del4232ins268, had been created by a non-homologous end joining (NHEJ). We conclude that MLPA is a convenient, rapid and reliable method for detection of intragenic deletions in the PAH gene and that a relatively high number of alleles with large deletions are present in the Slavic PKU population.
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Affiliation(s)
- Libor Kozak
- Center of Molecular Biology and Gene Therapy, University Hospital Brno, Czech Republic.
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