scholarly journals Detection of a Novel Mutation on the Gene ESCO2 in a Pediatric Patient with Syndactyly

Author(s):  
Nguyen Thy Ngoc ◽  
Le Thi Van Anh ◽  
Nguyen Thuy Duong ◽  
Nong Van Hai

Syndactyly is a congenital disease caused by the limb formation abnormalities during fetal development. In this research, we studied the genetic mutations in a pediatric patient with 3rd  and 4th fingers were fused together, symmetrically using the whole exome sequencing techniques based on Next generation sequencing. The obtained data revealed a novel mutation located in exon 11 of the gene ESCO2: c.1745A>G: p.582K>R. Sequence verification by Sanger sequencing confirmed the existence of this mutation in the patient as heterozygous form. In silico prediction using PredictSNP, PhD-SNP, PROVEAN or Polyphen-2 tools indicated that the mutation was likely to affect the structure and function of Acetyltransferase? (encoded by ESCO2 gene). Further studies will be performed to analyze the effect of this mutations on the intracellular protein network associated with syndactyly.

Author(s):  
Meryem Alagoz ◽  
Nasim Kherad ◽  
Sureyya Bozkurt ◽  
Adnan Yuksel

Purpose. Early infantile epileptic encephalopathy (EIEE) 57 belongs to a group of encephalopathies with early-onset and characterised by severe electroencephalogram abnormalities, seizures, developmental delay and intellectual disability. Method. We carried out Whole Exome analysis using Next Generation Sequencing (NGS) and bioinformatic analysis performed to find mutation associated with the patient phenotypes. The effect of the mutation on protein structure analysed by PolyPhen2 and Swissmodel ExPASy. Results. In this study, we evaluated two unrelated Turkish males diagnosed with EIEE type 57 to investigate the genetic cause of this disease. Whole exome sequencing revealed mutations in KCN2 gene, which is a member of Potassium channels (KCN) gene family associated with epileptic encephalopathies. Two mutations, c.545A>T (p.Asn182Ile and c.2638C>A (p.Leu880Met) were reported here as a novel mutation. Conclusions. Our findings implicate the genotype-phenotype correlation of these mutations. Furthermore, the computational analysis showed their effect on protein binding site and function suggesting their role in the development of early infantile epileptic encephalopathy 57.


2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Takumi Miura ◽  
Satoshi Yasuda ◽  
Yoji Sato

Abstract Background Next-generation sequencing (NGS) has profoundly changed the approach to genetic/genomic research. Particularly, the clinical utility of NGS in detecting mutations associated with disease risk has contributed to the development of effective therapeutic strategies. Recently, comprehensive analysis of somatic genetic mutations by NGS has also been used as a new approach for controlling the quality of cell substrates for manufacturing biopharmaceuticals. However, the quality evaluation of cell substrates by NGS largely depends on the limit of detection (LOD) for rare somatic mutations. The purpose of this study was to develop a simple method for evaluating the ability of whole-exome sequencing (WES) by NGS to detect mutations with low allele frequency. To estimate the LOD of WES for low-frequency somatic mutations, we repeatedly and independently performed WES of a reference genomic DNA using the same NGS platform and assay design. LOD was defined as the allele frequency with a relative standard deviation (RSD) value of 30% and was estimated by a moving average curve of the relation between RSD and allele frequency. Results Allele frequencies of 20 mutations in the reference material that had been pre-validated by droplet digital PCR (ddPCR) were obtained from 5, 15, 30, or 40 G base pair (Gbp) sequencing data per run. There was a significant association between the allele frequencies measured by WES and those pre-validated by ddPCR, whose p-value decreased as the sequencing data size increased. By this method, the LOD of allele frequency in WES with the sequencing data of 15 Gbp or more was estimated to be between 5 and 10%. Conclusions For properly interpreting the WES data of somatic genetic mutations, it is necessary to have a cutoff threshold of low allele frequencies. The in-house LOD estimated by the simple method shown in this study provides a rationale for setting the cutoff.


2020 ◽  
Author(s):  
Weiwei Yu ◽  
Haiqiang Jin ◽  
Jianwen Deng ◽  
Ding Nan ◽  
Yining Huang

Abstract Background: Hereditary spastic paraplegia is a heterogeneous group of clinically and genetically neurodegenerative diseases characterized by progressive gait disorder. Hereditary spastic paraplegia can be inherited in various ways, and all modes of inheritance are associated with multiple genes or loci. At present, more than 76 disease-causing loci have been identified in hereditary spastic paraplegia patients. Here, we report a novel mutation in SPAST gene associated with hereditary spastic paraplegia in a Chinese family, further enriching the hereditary spastic paraplegia spectrum. Methods: Whole genomic DNA was extracted from peripheral blood of the 15 subjects from a Chinese family using DNA Isolation Kit. The Whole Exome Sequencing of the proband was analyzed and the result was identified in the rest individuals. RaptorX prediction tool and Protein Variation Effect Analyzer were used to predict the effects of the mutation on protein tertiary structure and function.Results: Spastic paraplegia has been inherited across at least four generations in this family, during which only four HSP patients were alive. The results obtained by analyzing the Whole Exome Sequencing of the proband exhibited a novel disease-associated in-frame deletion in the SPAST gene, and the this mutation also existed in the rest three HSP patients in this family. This in-frame deletion consists of three nucleotides deletion (c.1710_1712delGAA) within the exon 16, resulting in lysine deficiency at the position 570 of the protein (p.K570del). This novel mutation was also predicted to result in the synthesis of misfolded SPAST protein and have the deleterious effect on the function of SPAST protein.Conclusion: In this case, we reported a novel mutation in the known SPAST gene that segregated with HSP disease, which can be inherited in each generation. Simultaneously, this novel discovery significantly enriches the mutation spectrum, which provides an opportunity for further investigation of genetic pathogenesis of HSP.


2021 ◽  
Author(s):  
Junyi Ouyang ◽  
Ziyan Cai ◽  
Yinjie Guo ◽  
Fen Nie ◽  
Mengdan Cao ◽  
...  

Abstract Background: Aniridia is a congenital,panocular disease affecting the cornea,anterior chamber angle,iris,lens,retina and optic nerve.PAX6 loss-of-function mutations were the most common cause of aniridia.Mutations throughout the PAX6 gene have been linked to a range of ophthalmic abnormalities,with distinct mutations at a given site within this gene leading to distinct phenotypic findings.This study aimed to characterize genetic mutations associated with congenital aniridia in a Chinese family. Methods: The proband and the proband’s brother of this family underwent comprehensive ophthalmologic examinations as well as exome sequencing,with Next Generation Sequencing being used to confirm these results. Results: A novel mutation(c.114_119delinsAATTTCC:p.Pro39fs)in the PAX6 gene was identified in subjects III-2 and III-3 in these family,and both of these subjects exhibited completeaniridia,cataracts,glaucoma,high myopia,and foveal hypoplasia. Conclusions We identified a novel PAX6 frameshift heterozygous deletion mutation in a Chinese family and determined that this mutation was a probable cause of various eye abnormalities in carriers.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 3344-3344
Author(s):  
Omar Niss ◽  
Satheesh Chonat ◽  
Karol Kerr ◽  
Patrick T. McGann ◽  
Marya Obaid Almansoori ◽  
...  

Abstract Hereditary elliptocytosis (HE) results from defects in the erythrocyte membrane proteins α-spectrin, β-spectrin or protein 4.1R that weaken the ÒhorizontalÓ cytoskeletal associations causing decreased mechanical stability and deformability of the red blood cell (RBC). The hallmark of HE is the presence of elliptical RBCs on peripheral blood smears. Diseases within the spectrum of HE include classic HE and hereditary pyropoikilocytosis (HPP). The traditional diagnosis of HE relies on visualization of elliptocytes on the blood smear, while HPP is characterized by significant poikilocytosis and abnormally shaped RBCs. In vitro assessment of RBC membrane biomechanical properties using ektacytometry is characteristic. However, this evaluation requires a pure RBC population, which may not be available in patients requiring frequent transfusions and does not predict disease course or severity. Using a Next-Generation sequencing panel for 12 genes associated with RBC membrane disorders, we identified the causative genetic mutations in 8 patients with clinically diagnosed or suspected HE or HPP (3 with HE and 5 with HPP). We correlated the identified genetic mutations with clinical presentation, blood smear findings, and ektacytometry results. HE patients: 2 patients with HE had heterozygous mutations in SPTA1 (p.L154_L155insL) resulting in spectrin self-association defect, while the third one had a novel nonsense heterozygous mutation in EPB41 (p.R262*) resulting in defective horizontal interaction between spectrin and actin in the RBC cytoskeleton due to decreased band 4.1R. The same novel mutation was identified in the patient's mother. Both, the patient and the mother, had smear findings and ektacytometry profiles consistent with the diagnosis of HE (Fig. 1A). HPP patients: 3 out of 5 HPP patients were found to be compound heterozygous for a SPTA1 mutation at the self-association site (p.R28H or p.L154_L155insL) and a low-expression SPTA1 allele (c.6531-12C>T known as α-LELY or Low Expression LYon) which allows for the expanded expression of the HE-causing mutation located in trans, resulting in a more severe phenotype. Of note, two siblings carried the same SPTA1 mutation (p.L154_L155insL); one was heterozygous and had mild HE while the other sibling carried α-LELY in trans to the HE-mutation causing a more severe anemia with poikilocytosis and worsened deformability consistent with HPP (Fig. 1B). The ektacytometry profile of these two siblingsÕ RBCs demonstrates the role of α-LELY in modifying the phenotype of elliptocytic disorders. A fourth patient with HPP was found to have compound heterozygosity for mutations in SPTA1 (p.L154_L155insL) and SPTB (p.W2024R) both in the self association sites between α- and β-spectrin. The fifth patient was a 3 y.o. boy with transfusion-dependent hemolytic anemia since infancy and therefore his erythrocyte phenotype could not be evaluated. He was homozygous for a novel mutation in SPTB (p.F2014V); both of his parents were heterozygous for the same mutation. The parents were asymptomatic but their ektacytometry profiles and blood smears were consistent with HE (Fig. 1C), indicating that this mutation in the b-spectrin dimerization domain alters the α- and β-spectrin interaction causing HE in heterozygous state and HPP in the homozygous state. Next-Generation sequencing for genetic diagnosis in HE and HPP can confirm or identify the diagnosis and may be helpful to predict the phenotype and clinical severity in these heterogeneous disorders. Combining clinical data, ektacytometry and family studies is important to understand the relevance of new genetic variants to pathology of RBC cytoskeletal disorders, provide insight into the genotype-phenotype correlation, and improve the genetic counseling and clinical care for these disorders. Figure1. Ektacytometry profiles of : A) a patient and his mother heterozygous for a novel nonsense mutation in EPB41 (p.R262*) causing HE, B) a patient with SPTA1 mutation (p.L154_L155insL) and α-LELY causing HPP compared to a sibling with the same heterozygous mutation in SPTA1 without α-LELY causing HE, C) novel mutation in SPTB (p.F2014V) causing mild HE to heterozygous parents but severe transfusion-dependent anemia in the homozygous child. Ektacytometry was not performed in the child since he was chronically transfused. Figure 1. Figure 1. Disclosures No relevant conflicts of interest to declare.


2020 ◽  
Vol 5 (1) ◽  
pp. 19-26
Author(s):  
Guangming Fang ◽  
Jinxin Miao ◽  
Ying Peng ◽  
Yafei Zhai ◽  
Chuchu Wang ◽  
...  

Objective: The purpose of this work was to obtain the phenotypes and detect potential mutations in three Chinese patients with Marfan syndrome (MFS) or incomplete MFS phenotypes.Methods: Three unrelated patients with a definite or suspected clinical diagnosis of MFS and their family members were recruited for research. Genomic DNA was extracted from peripheral blood of these patients and their family members. All the exons were sequenced by next-generation sequencing and the variants were further validated by Sanger sequencing. The functional consequences of the mutations were analyzed with various genomic resources and bioinformatics tools.Results: Three FBN1 mutations were identified in the three patients, including one novel mutation (2125G > A) and two previously reported mutations (4786C > T and 6325C > T). It was interesting to note that the parents of these patients were normal as assessed by clinical features or genetic testing, but all these mutations were detected in their offspring, except for the variant 6325C > T. We also found that a few young members of the family of probands (proband 1 and proband 2) have exhibited no manifestations of MFS so far, although they carry the same disease-causing mutation.Conclusions: We found three FBN1 mutations in three unrelated Chinese families with MFS by genome sequencing, and the relationship between genotypes and phenotypes in MFS patients needs further exploration.


2020 ◽  
Author(s):  
Junyi Ouyang ◽  
Ziyan Cai ◽  
Yinjie Guo ◽  
Fen Nie ◽  
Mengdan Cao ◽  
...  

Abstract Background Aniridia is a congenital,panocular disease affecting the cornea,anterior chamber angle,iris,lens,retina and optic nerve.PAX6 loss-of-function mutations were the most common cause of aniridia.Mutations throughout the PAX6 gene have been linked to a range of ophthalmic abnormalities,with distinct mutations at a given site within this gene leading to distinct phenotypic findings.This study aimed to characterize genetic mutations associated with congenital aniridia in a Chinese family.MethodsThe proband and the proband’s brother of this family underwent comprehensive ophthalmologic examinations as well as exome sequencing,with Next Generation Sequencing being used to confirm these results.Results A novel mutation(c.114_119delinsAATTTCC:p.Pro39fs)in the PAX6 gene was identified in subjects III-2 and III-3 in these family,and both of these subjects exhibited completeaniridia,cataracts,glaucoma,high myopia,and foveal hypoplasia.Conclusions We identified a novel PAX6 frameshift heterozygous deletion mutation in a Chinese family and determined that this mutation was a probable cause of various eye abnormalities in carriers.


2020 ◽  
Author(s):  
Weiwei Yu ◽  
Haiqiang Jin ◽  
Jianwen Deng ◽  
Ding Nan ◽  
Yining Huang

Abstract Background: Hereditary spastic paraplegia is a heterogeneous group of clinically and genetically neurodegenerative diseases characterized by progressive gait disorder. Hereditary spastic paraplegia can be inherited in various ways, and all modes of inheritance are associated with multiple genes or loci. At present, more than 76 disease-causing loci have been identified in hereditary spastic paraplegia patients. Here, we report a novel mutation in SPAST gene associated with hereditary spastic paraplegia in a Chinese family, further enriching the hereditary spastic paraplegia spectrum. Methods: Whole genomic DNA was extracted from peripheral blood of the 15 subjects from a Chinese family using DNA Isolation Kit. The Whole Exome Sequencing of the proband was analyzed and the result was identified in the rest individuals. RaptorX prediction tool and Protein Variation Effect Analyzer were used to predict the effects of the mutation on protein tertiary structure and function.Results: Spastic paraplegia has been inherited across at least four generations in this family, during which only four HSP patients were alive. The results obtained by analyzing the Whole Exome Sequencing of the proband exhibited a novel disease-associated in-frame deletion in the SPAST gene, and the this mutation also existed in the rest three HSP patients in this family. This in-frame deletion consists of three nucleotides deletion (c.1710_1712delGAA) within the exon 16, resulting in lysine deficiency at the position 570 of the protein (p.K570del). This novel mutation was also predicted to result in the synthesis of misfolded SPAST protein and have the deleterious effect on the function of SPAST protein.Conclusion: In this case, we reported a novel mutation in the known SPAST gene that segregated with HSP disease, which can be inherited in each generation. Simultaneously, this novel discovery significantly enriches the mutation spectrum, which provides an opportunity for further investigation of genetic pathogenesis of HSP.


2021 ◽  
Vol 9 ◽  
Author(s):  
Yu-Xing Liu ◽  
Ai-Qian Zhang ◽  
Fang-Mei Luo ◽  
Yue Sheng ◽  
Chen-Yu Wang ◽  
...  

Idiopathic focal segmental glomerulosclerosis (FSGS) is a relatively frequent kidney disorder that manifest clinically as proteinuria and progressive loss of renal function. Genetic factors play a dominant role in the occurrence of FSGS. CD2-associated protein (CD2AP) is an adapter molecule and is essential for the slit-diaphragm assembly and function. Mutations in the CD2AP gene can contribute to FSGS development. Here, we describe a Chinese family of four generations with unexplained proteinuria. The proband, a 12-year-old boy, was diagnosed as FSGS. Whole-exome sequencing (WES) revealed an unknown frameshift insertion mutation (p.K579Efs*7) of CD2AP gene that leads to a truncation of CD2AP protein. Bioinformatics strategies predicted that the novel mutation was pathogenic. The mutation was absent in either healthy family members or our 200 healthy controls. In summary, we used WES to explore the genetic lesion of FSGS patients and identified a novel mutation in CD2AP gene. This work broadens the mutation spectrum of CD2AP gene and provides data for genetic counseling to additional FSGS patients.


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