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Objective:To explore application status and development trend of spinal muscular atrophy (SMA) genetic diagnosis technology based on the national rare diseases registry system of China.Method:A total of 200 SMA children registered at the Capital Institute of Pediatrics from July 2016 to December 2018 were included in this retrospective cross-sectional survey. The basic data, clinical subtypes, genotypes, and related genetic testing information of SMA children were obtained by checking SMA registration information, genetic testing reports, and also by telephone follow-up. The patient number and the composition of different genetic diagnosis technologies were analyzed by the stratification of genetic testing at various time. The correlation between the proportion of genetic diagnosis technology and genetic testing time was analyzed with Pearson correlation analysis.Result:There were 3 SMA cases with incomplete data, the remaining 197 SMA cases were included in this study. There were 37 (18.8%), 115 (58.4%) and 45 (22.8%) patients with type Ⅰ, Ⅱ and Ⅲ SMA, respectively. There were 185 cases of SMN1 homozygous deletion (93.9%), and 12 cases with compound heterozygotes (6.1%). Seven SMA-related genetic technologies were used from 2004 to 2017. MLPA accounted for 54.1% (100/185) used approach, followed by PCR-RFLP and first-generation sequencing, which accounted for 22.7% (42/185) and 10.3% (19/185), respectively. Nine, 6, 5 and 4 cases were tested with AS-PCR, qPCR, WES and DHPLC, respectively (2.2%-4.9%). The proportion of MLPA increased gradually since 2010 ( r=0.95, P<0.05), while PCR-RFLP declined gradually since 2004 ( r=-0.99, P<0.05). No correlation was found between technology and testing time for other genetic testing technologies ( P>0.05). The proportion of quantitative genetic technologies (MLPA, qPCR and DHPLC) increased gradually since 2010 ( r=0.94, P<0.05), and qualitative genetic technologies (PCR-RFLP, first-generation sequencing, AS-PCR and WES) decreased gradually since 2004 ( r=-0.94, P<0.05). The duplication detection rates of homozygous deletion and compound heterozygous mutation were 12.4% (23/185) and 41.7% (5/12), respectively (χ 2=5.86, P<0.05). During 2008-2015, the proportion of "the reports of both copy numbers of SMN1 gene and SMN2 gene" increased from 56.8% (21/37) in 2008-2015 to 69.1% (56/81) in 2016-2017. Conclusion:Genetic diagnosis of SMA has gradually developed from qualitative detection technology to quantitative detection technology, such as MLPA and qPCR, in China. In more and more SMA quantitative test reports, quantitative results of SMN2 gene are also provided in addition to quantitative results of SMN1 gene.
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<p><b>OBJECTIVE</b>To establish a hyperphenylalaninemia related genes screening method using Ion Torrent Personal Genome Machine (PGM) for early detection and differential diagnosis of hyperphenylalaninemia (HPA).</p><p><b>METHODS</b>Three children with known HPA mutations and a healthy control were used for setting up the method. Ten children with HPA with known mutations were recruited for validating the method. Ion Ampliseq PCR was used to amplify the 5' and 3' untranslated region, coding sequence, and flanking introns of PAH, GCH1, PTS, QDPR, and PCBD1 genes. After the enrichment with the Ion OneTouch system, the products were sequenced by PGM. Data from the PGM were processed with Torrent Suite v2.2 software package. All variations were confirmed by Sanger sequencing.</p><p><b>RESULTS</b>For the 4 samples, the PGM output was 94.22 Mb, with approximately 99.5% of reads mapping to the target regions. Among these samples, we detected 74 variations (28 positions) including 6 known mutations. Compared with database and results of Sanger sequencing, 55 (18 positions) polymorphisms and 13 (4 positions) false positive calls were confirmed. For the 10 samples, all the known mutations were successfully identified.</p><p><b>CONCLUSION</b>Ion Torrent PGM sequencing is suitable for screening genetic mutation underlying HPA from the perspective of metabolic pathways, which can meet the clinical demand for individualized diagnosis and treatment.</p>
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Humans , High-Throughput Nucleotide Sequencing , Methods , Mutation , Phenylketonurias , GeneticsABSTRACT
Objective To analyze the distribution of common chromosomal karyotypes of patients with Turner syndrome (TS), and to explore the correlation between the age and height standard deviation scores (HSDS) on diagnosis.Methods Retrospective investigation was performed for the data of age and HSDS on diagnosis in 273 TS girls(≤ 18.0 years old)diagnosed by chromosomal karyotypes.The main statistical methods were analyzed with t-test and Pearson correlation test by using the SPSS 18.0 statistical software.Results (1) There were 4 kinds of common chromosomal karyotypes in the TS :45, X (87/273 cases,31.9％),46, X, i (Xq) (43/273 cases, 15.7％) ,45, X/46, X, i (Xq) (36/273 cases, 13.2％) and 45, X/46, XX (23/273 cases, 8.4％), respectively, the adolescent TS all had delayed puberty.For the cases with 45, X karyotypes ,3 cases presented mental retardation and 2 cases with organs deformity.(2)The patients with 45 ,X/46,X,i(Xq) karyotypes or with 46,X,i(Xq) karyotypes had the maximum(12.56 age) or the minimum(9.70 age) mean age on diagnosis, respectively, there was a significant difference between 2 groups (t =3.019, P =0.004).The maximum deviation from normal height was found in the patients with karyotypes of 46, X,i (Xq) (HSDS =-4.04), and the minimum deviation was in the patients with karyotypes of 45,X/46, XX (HSDS =-3.16), and there was a significant difference between 2 groups (t =-2.95, P =0.004).(3) More than 75.7％ of TS patients was diagnosed when their heights deviated above 3 SD,and their mean age on diagnosis was 12.10 age,which was 3 years later than those patients within 2 SD.(4) There was a significant negative correlation between the age and HSDS on diagnosis in the groups of common chromosomal karyotypes[45,X、46,X,i(Xq) and 45,X/46,XX] (r =-0.551,-0.560,-0.622,all P ＜ 0.01), except for the group with the 45, X/46, X, i (Xq).Conclusions (1) In this study, the consti-tuent ratios of these 4 common chromosomal karyotypes were different from those in Europe and America's.(2)Patients with 45 ,X may have more severe symptoms than others.(3)The mean age on diagnosis was at least 3.0 years earlier when considered HSDS below-2.00 as an indicator for chromosomal karyotype screening,which would facilitate earlier diagnosis.
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Objective To perform mutation analysis of survival motor neuron gene 1 (SMN1 in two spinal muscular atrophy (SMA) patients and their parents to evaluate the effects of the two SMN1 gene mutations on the transcript levels of the gene and preliminarily predict their effects on the structure and function of SMN protein.Methods Mutation analysis of SMN1 gene was carried out by multiplex ligationdependent probe amplification,reverse transcript-polymerase chain reaction (RT-PCR) and cloning sequencing.Transmission of the mutations was confirmed by the mutation analysis in patients' parents.The full-length SMN1 (SMN1-fl) transcript levels of the patients carrying these subtle mutations were detected using quantitative RT-PCR.Results The two patients were diagnosed as SMA Ⅱ and SMA Ⅲ.They carried p.Val19GlyfsX21 and p.Ala2Gly SMN1 mutations in SMN1 gene,respectively.Both of the two mutations were originated from their fathers.Compared with the healthy individuals (23.5 ± 4.9),the two patients had a significant reduction in the level of SMN1-fl transcripts (t =3.322,P =0.011 (p.Ala2Gly) ;t =6.964,P =0.000 (p.Val19GlyfsX21)).However,compared with the healthy carriers (14.1 ±4.5),the patient with p.Ala2Gly mutation had no significant reduction in the level of SMN1-fl transcripts (13.9 ±3.6,t =0.058,P =0.955) ; however,the patient with p.Val19GlyfsX21 mutation had a significant reduction (4.9± 2.4,t =3.725,P =0.004).Conclusions Two SMN1 gene mutations are identified in our study.The mutation p.Val19GlyfsX21 is a novel mutation and p.Ala2Gly is firstly reported in Chinese SMA patients.p.Val19GlyfsX21 may possibly lead to decreased SMN1-fl mRNA by nonsense-mediated messenger RNA decay,however,p.Ala2Gly has no obvious effects on the amount of the SMN1-fl transcripts,indicating that its deleterious effect may be occurring at SMN protein level or the function of SMN protein.
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<p><b>OBJECTIVE</b>To understand the pathogenic effect and the correlation between the genotype and phenotype of the 4 novel missense mutations (G247S, E280G, P362T and A434D) of phenylalanine hydroxylase gene (PAH).</p><p><b>METHODS</b>(1) The enzyme activity of the 4 mutants was assessed by using transient protein expression in mammalian cells. (2) The PAH amino acid sequences among different animal species were alignmented. (3) The effects of the 4 missense mutations on the protein structure were analyzed. (4) The clinical phenotype of the patients with PKU were analyzed, according to their blood Phe levels prior to treatment and the Phe tolerance.</p><p><b>RESULTS</b>(1) The residual enzyme activity expressed in vitro of G247S, E280G, P362T and A434D were 3.1%, 0.4%, 8.2% and 21.7% of the wild-type PAH respectively; (2)Gly247, Glu280 and Pro362 were among the highly conserved amino acids, while Ala434 was only moderately conserved; (3) As revealed by 3D structural analysis, G247S and E280G, being located at the active center of the enzyme, interfered with the binding of PAH to BH4 and ferrousion respectively, while P362T and A434D affected the formation and stability of the dimer and the tetramer of PAH; (4) As shown by clinical phenotypic analysis, classical PKU were observed in patients carrying G247S and E280G, moderate PKU were observed in patients carrying A434D, whereas both classical and moderate PKU were observed in patients carrying P362T.</p><p><b>CONCLUSION</b>(1) The E280G, G247S, P362T and A434D are all disease-causing mutations, with those located at the center of the enzyme displaying the most marked pathogenic effect; (2)The results of the structural analysis of the 3D molecule are consistent with the activity assessment of the enzyme expressed in vitro; (3) The consistency is observed between the genotype, the enzymatic activity expressed in vitro and the clinical phenotype.</p>
Subject(s)
Animals , Child , Child, Preschool , Female , Humans , Infant , Infant, Newborn , Male , Amino Acid Sequence , Gene Expression , Genotype , Models, Molecular , Molecular Sequence Data , Mutant Proteins , Chemistry , Genetics , Metabolism , Mutation, Missense , Phenotype , Phenylalanine Hydroxylase , Chemistry , Genetics , Metabolism , Phenylketonurias , Genetics , Protein Conformation , Sequence Alignment , Structure-Activity RelationshipABSTRACT
Objective To study the mutation characteristics in phenylalanine hydroxylase gene of Xinjiang minority nationality phenylketonuria (PKU) patients and provide a scientific basis for PKU prevention and cure strategy.Methods Mutations in phenylalanine hydroxylase gene were detected by Dolymerase chain reaction-single strand comformation polymorphism (PCR/SSCP) and gene sequencing in 12 minoritv nationality patients.Results Thirteen different mutations,including 8 missense mutations,1 nonsense mutation and 3 splice mutations were found in 24 alleles.The moat common mutations were EX696A＞G and P281 L.which were respectively prevalent in Asia and Europe populations.The common mutations were R243Q,R111X,R176X and F161S.The mutation frequency of R243Q was the highest and R111X was the third highest in Northern China.R176X and F161S were two rare mutations world wide.Especially.F161S was a Chinese-specific mutation because it was for the second time that it was found in China.The mutations detected in this study were first reported in these 3 minority nationality populations,which showed a distinct ethical characteristic.Condusions There is not only a consanguineous relation but also a distinct difference in PAH gene distribution between Xinjiang minority nationality population and yellow race and Latin-American.The results suggest that Xinjiang could probably be a special PAH gene distribution region.
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BACKGROUND: Phenylketonuria is caused by gene mutation of phenylalanine hydroxylasel (PAH), which is mainly induced by permutation, short segments and insertion of base.OBJECTIVE: To evaluate the gene mutation of phenylalanine hydroxylasel in phenylketonuria in Hui nationality.DESIGN: Open study.SETTING: Urumqi General Hospital of Lanzhou Military Area Command of Chinese PLA; Capital Pediatrics Institute.PARTICIPANTS: A boy of Hui nationality in China and aged 3.1 years was selected in this study. The boy had intellect hysteresis in his one year and received medical treatment in his three years, while he was diagnosed as cerebral paralysis. After repeatedly inefficient treatment, he was hospitalized in our hospital on December 13, 2004. Iron sesquichloride in urine was strongly positive and concentration of serum phenylalanine was 1 680 μmol/L; therefore, he was diagnosed as the typical phenylketonuria.METHODS: 5 mL venous blood was selected from the boy and his parents, respectively, and anticoagulated with EDTA-Na2. DNA in gene group was extracted by using typical phenol/chloroform method. In addition, polymerase chain reaction (PCR) primer sequence of extron 7, 6, 11, 3, 12 and 5 of PAH gene was designed based on references. And then, PCR products were detected with 2% agarose gel electrophoresis. 5 μL PCR products were mixed with the same volume of degenerated buffer solution, degenerated at 97 ℃ for 5 minutes, put in iced bath and performed with 80 g/Lnon-degenerated polyacrylamide gel electrophoresis. After that, the products were dealt with sliver staining routinely, and single strand DNA banding patterns were analyzed and recorded. ABI377 automatic sequenator (PE Company) was used to detect PCR sequence and purify PCR product in Shanghai Boya Biotechnology Company.MAIN OUTCOME MEASURES: Iron sesquichloride in urine, concentration of serum phenylalanine and mutant gene types of phenylalanine hydroxylase.RESULTS: Extron 7, 6, 11, 3, 12 and 5 of PAH gene were analyzed in the boy and his parents. The results demonstrated that SSCP electrophoresis in extron 6 was different from that in the normal control group. Site of electrophoresis strip of his father was coincident with that of his mother, but different from that of the boy. Sequencing results indicated that point mutation (cytosine replaced by thymine), which was a R176X mutant heterozygote, occurred at the 526th site of cDNA of phenylalanine hydroxylase gene in his parents; however, two chromosomes of the boy had mutation at the same site, which was R176X mutant homozygote.CONCLUSION: Mutation of R176X homozygote of phenylketonurea is firstly reported in Hui nationality in China.
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Objective To perform PCR site-directed mutagenesis of nine novel PAH gene mutations (Y154H, R157I, Y206C, G247R, D282G, G346R, S349A, A389G, R400K) identified in northern Chinese and construct mutant recombinant plasmids of PAH gene. Methods 1) Every mutant recombinant plasmid was constructed according to the site of the mutation localized in functional domain of PAH gene and the related clinic phenotype of patients with the gene mutation. 2) Using the wild-type PAH expression vector as a templet, the mutant recombinant plasmids were directly amplified by PCR with Platinium Taq DNA polymerase and nine pairs of primers which were designed according to the human PAH cDNA sequence and the requirement for site-directed mutagenesis technology. 3) The positive strains were selected by Amp resistant test, PCR and restriction endonuclease analysis. The Mva Ⅰ, Mva Ⅰ, Hind Ⅲ, Rsa Ⅰ, Rsa Ⅰ sites exist in the sequences near the mutant sites of S349A, D282G, G247R, Y206C, Y154H, respectively, but not in the related sequence of wild-type PAH expression vector. Restriction endonuclease digestion could be directly used in identifying the mutant sites. However, the amplification created restriction site (ACRS) analysis was supplied in the followed identification of R157I, G346R, A389G, R400K. Finally the sequences of mutant recombinant plasmids of PAH gene were confirmed by DNA sequence analysis. Results Every sequence analysis showed that the mutant nucleic acids were introduced at the expected sites of PAH gene, suggesting that the mutant recombinant plasmids of PAH gene were constructed successfully. Conclusion PCR site-directed mutagenesis is accurate and highly efficient. The successfully mutagenized plasmids of PAH gene lay the foundation for the functional analysis of phenylalanine hydroxylase in mammalian cell system.