1
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Liu Y, Liu Y, Guo L, Wu Y, Wang Y, Xu L, Xu M, Huang S, Chen P, Wang T, Huang Q, Li Q. Multiplex Asymmetric PCR by Combining the Amplification Refractory Mutation System with the Homo-Tag-Assisted Nondimer System. Anal Chem 2024; 96:9200-9208. [PMID: 38771984 DOI: 10.1021/acs.analchem.4c01322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Asymmetric PCR is widely used to produce single-stranded amplicons (ss-amplicons) for various downstream applications. However, conventional asymmetric PCR schemes are susceptible to events that affect primer availability, which can be exacerbated by multiplex amplification. In this study, a new multiplex asymmetric PCR approach that combines the amplification refractory mutation system (ARMS) with the homo-Tag-assisted nondimer system (HANDS) is described. ARMS-HANDS (A-H) PCR utilizes equimolar-tailed forward and reverse primers and an excess Tag primer. The tailed primer pairs initiate exponential symmetric amplification, whereas the Tag primer drives linear asymmetric amplification along fully matched strands but not one-nucleotide mismatched strands, thereby generating excess ss-amplicons. The production of ss-amplicons is validated using agarose gel electrophoresis, sequencing, and melting curve analysis. Primer dimer alleviation is confirmed by both the reduced Loss function value and a 20-fold higher sensitivity in an 11-plex A-H PCR assay than in an 11-plex conventional asymmetric PCR assay. Moreover, A-H PCR demonstrates unbiased amplification by its allele quantitative ability in correct identification of all 31 trisomy 21 samples among 342 clinical samples. A-H PCR is a new generation of multiplex asymmetric amplification approach with various applications, especially when sensitive and quantitative detection is required.
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Affiliation(s)
- Ying Liu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yinghua Liu
- Centre for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215002, China
| | - Liu Guo
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yazhe Wu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yafang Wang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Lingzhen Xu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Mingzhu Xu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Siyu Huang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Ping Chen
- NHC Key Laboratory of Thalassemia Medicine, Key Laboratory of Thalassemia Medicine, Chinese Academy of Medical Sciences, Guangxi Key Laboratory of Thalassemia Research, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Ting Wang
- Centre for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou 215002, China
| | - Qiuying Huang
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen 361102, China
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2
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Ha C, Jang JH, Kim YG, Kim JW. Reclassification of variants of tumor suppressor genes based on Sanger RNA sequencing without NMD inhibition. Front Genet 2023; 14:1283611. [PMID: 37900184 PMCID: PMC10602670 DOI: 10.3389/fgene.2023.1283611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction: RNA sequence analysis can be effectively used to identify aberrant splicing, and tumor suppressor genes are adequate targets considering their loss-of-function mechanisms. Sanger sequencing is the simplest method for RNA sequence analysis; however, because of its insufficient sensitivity in cases with nonsense-mediated mRNA decay (NMD), the use of cultured specimens with NMD inhibition has been recommended, hindering its wide adoption. Method: The results of Sanger sequencing of peripheral blood RNA without NMD inhibition performed on potential splicing variants of tumor suppressor genes were retrospectively reviewed. For negative cases, in which no change was identified in the transcript, the possibility of false negativity caused by NMD was assessed through a review of the up-to-date literature. Results: Eleven potential splice variants of various tumor suppressor genes were reviewed. Six variants were classified as pathogenic or likely pathogenic based on the nullifying effect identified by Sanger RNA sequencing. Four variants remained as variants of uncertain significance because of identified in-frame changes or normal expression of both alleles. The result of one variant was suspected to be a false negative caused by NMD after reviewing a recent study that reported the same variant as causing a nullifying effect on the affected transcript. Conclusion: Although RNA changes found in the majority of cases were expected to undergo NMD by canonical rules, most cases (10/11) were interpretable by Sanger RNA sequencing without NMD inhibition due to incomplete NMD efficiency or allele-specific expression despite highly efficient NMD.
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3
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Zhao S, Duan Y, Ma L, Shi Q, Wang K, Zhou Y. Sudden death due to a novel nonsense mutation in Marfan syndrome. Leg Med (Tokyo) 2021; 53:101967. [PMID: 34598112 DOI: 10.1016/j.legalmed.2021.101967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/16/2021] [Accepted: 09/18/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND Marfan syndrome is a hereditary connective tissue disease accompanied by autosomal dominant inheritance; that mainly arises from a mutation in the fibrillin-1 gene (FBN1). Aortic dissection and rupture are the common and lethal complications of MFS and may cause sudden unexpected death. METHOD A man aged 34 was admitted to the hospital due to persistent pain in his abdomen 12 h post-drinking and suddenly died 10 h later. A forensic autopsy was performed to identify the underlying mechanism of death. Due to the high suspected of MFS, Sanger sequencing was performed, and a novel mutation was detected in the deceased. To clarify the underlying mechanism of this mutation, real-time quantitative polymerase chain reaction was conducted and Western blot analysis was performed in vitro. RESULTS A novel PTC mutation c.933C > A in FBN1 was found. Through family history inspection and Sanger sequencing, other MFS patients in the present family were confirmed. The pathologic changes in the aorta in the present case showed media cystic degeneration, disordered arrangement of elastic fibers and a significant reduction in fibrillin 1 compared with the control. The mutation led to significant reduction inFBN1 mRNA and fibrillin-1 in cells in vitro, and overexpression of phospho-Smad2 was observed. CONCLUSION We confirmed a novel pathogenic PTC mutation in the FBN1gene through Sanger sequencing, and the pathological changes and underlying mechanisms were also identified. The present work not only extends the pathogenic mutation spectrum of MFS, but also stresses the role of forensic autopsy, genetic analysis and functional validation of novel mutations in cases of sudden death associated with congenital diseases.
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Affiliation(s)
- Shuquan Zhao
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Wuhan 430030, PR China.
| | - Yijie Duan
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Wuhan 430030, PR China
| | - Longda Ma
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Wuhan 430030, PR China
| | - Qing Shi
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Wuhan 430030, PR China
| | - Kang Wang
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Wuhan 430030, PR China.
| | - Yiwu Zhou
- Department of Forensic Medicine, Tongji Medical College, Huazhong University of Science and Technology, No. 13 Hangkong Road, Wuhan 430030, PR China.
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4
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Erhart P, Gieldon L, Ante M, Körfer D, Strom T, Grond-Ginsbach C, Böckler D. Acute Stanford type B aortic dissection-who benefits from genetic testing? J Thorac Dis 2020; 12:6806-6812. [PMID: 33282382 PMCID: PMC7711383 DOI: 10.21037/jtd-20-2421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Background Stanford type B aortic dissection is a rare, life-threatening complex phenotype associated with several modifiable and genetic risk factors. In the current study of a hospital-based, consecutive series of aortic dissection patients we propose a selection based on age and family history of aortic disease for genetic testing and detection of causative gene variants. Methods In this single center cohort study from 2013 to 2018 patients with acute Stanford type B aortic dissections were consecutively treated and analyzed by next generation sequencing based on selection criteria (age of disease onset ≤45 years and/or positive familial history for aortic disease) to detect genome-wide pathogenic variants in protein-coding sequences and to identify large copy number variants (CNV). Variants in a predefined panel of 30 genes associated with the familial thoracic aortic aneurysm and dissection (TAAD) syndrome were evaluated. Results From 105 patients nine matched selection criteria for genetic testing. Next-generation sequencing analysis revealed causal variants in FBN1 (fibrillin-1) in three patients: a pathogenic missense variant [c.6661T>C, p.(Cys2221Arg)] and two truncating variants [c.4786C>T, p.(Arg1596Ter)] and [c.6366C>CA, p.(Asp2123GlufsTer5)]. A fourth patient carried a large (>1,000,000 bp) CNV in the long arm of chromosome 10, deleting eleven genes, including the whole ACTA2 (actin alpha 2) gene. The latter two genetic findings have not been reported before. Conclusions Selection of patients on the basis of young age and familial inheritance of aortic disease favors the identification of disease-causing genetic variants in a clinical cohort of patients with Stanford type B aortic dissection.
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Affiliation(s)
- Philipp Erhart
- Department of Vascular and Endovascular Surgery, Ruprechts-Karls University Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Laura Gieldon
- Institute of Human Genetics, Ruprecht-Karls University Heidelberg, Im Neuenheimer Feld 440, 69120 Heidelberg, Germany
| | - Marius Ante
- Department of Vascular and Endovascular Surgery, Ruprechts-Karls University Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Daniel Körfer
- Department of Vascular and Endovascular Surgery, Ruprechts-Karls University Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Tim Strom
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Caspar Grond-Ginsbach
- Department of Vascular and Endovascular Surgery, Ruprechts-Karls University Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
| | - Dittmar Böckler
- Department of Vascular and Endovascular Surgery, Ruprechts-Karls University Heidelberg, Im Neuenheimer Feld 420, 69120 Heidelberg, Germany
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5
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Fang G, Miao J, Peng Y, Zhai Y, Wang C, Zhao X, Wang Y, Dong J. Identification of Three FBN1 Mutations in Chinese Patients with Typical or Incomplete Marfan Syndrome by Whole-Exome Sequencing. CARDIOVASCULAR INNOVATIONS AND APPLICATIONS 2020. [DOI: 10.15212/cvia.2019.0576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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.
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Affiliation(s)
- Guangming Fang
- Department of Cardiology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan 450052, P. R. China
| | - Jinxin Miao
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, Henan 450046, P. R. China
| | - Ying Peng
- Department of Cardiology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan 450052, P. R. China
| | - Yafei Zhai
- Department of Cardiology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan 450052, P. R. China
| | - Chuchu Wang
- College of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450000, P. R. China
| | - Xiaoyan Zhao
- Department of Cardiology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan 450052, P. R. China
| | - Yaohe Wang
- Sino-British Research Center for Molecular Oncology, National Center for the International Research in Cell and Gene Therapy, School of Basic Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450052, P. R. China
| | - Jianzeng Dong
- Department of Cardiology, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan 450052, P. R. China
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6
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Najafi A, Caspar SM, Meienberg J, Rohrbach M, Steinmann B, Matyas G. Variant filtering, digenic variants, and other challenges in clinical sequencing: a lesson from fibrillinopathies. Clin Genet 2020; 97:235-245. [PMID: 31506931 PMCID: PMC7004123 DOI: 10.1111/cge.13640] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/04/2019] [Accepted: 09/07/2019] [Indexed: 12/23/2022]
Abstract
Genome-scale high-throughput sequencing enables the detection of unprecedented numbers of sequence variants. Variant filtering and interpretation are facilitated by mutation databases, in silico tools, and population-based reference datasets such as ExAC/gnomAD, while variants are classified using the ACMG/AMP guidelines. These methods, however, pose clinically relevant challenges. We queried the gnomAD dataset for (likely) pathogenic variants in genes causing autosomal-dominant disorders. Furthermore, focusing on the fibrillinopathies Marfan syndrome (MFS) and congenital contractural arachnodactyly (CCA), we screened 500 genomes of our patients for co-occurring variants in FBN1 and FBN2. In gnomAD, we detected 2653 (likely) pathogenic variants in 253 genes associated with autosomal-dominant disorders, enabling the estimation of variant-filtering thresholds and disease predisposition/prevalence rates. In our database, we discovered two families with hitherto unreported co-occurrence of FBN1/FBN2 variants causing phenotypes with mixed or modified MFS/CCA clinical features. We show that (likely) pathogenic gnomAD variants may be more frequent than expected and are challenging to classify according to the ACMG/AMP guidelines as well as that fibrillinopathies are likely underdiagnosed and may co-occur. Consequently, selection of appropriate frequency cutoffs, recognition of digenic variants, and variant classification represent considerable challenges in variant interpretation. Neglecting these challenges may lead to incomplete or missed diagnoses.
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Affiliation(s)
- Arash Najafi
- Center for Cardiovascular Genetics and Gene DiagnosticsFoundation for People with Rare DiseasesSchlieren‐ZurichSwitzerland
- Cantonal Hospital WinterthurInstitute of Radiology and Nuclear MedicineWinterthurSwitzerland
| | - Sylvan M. Caspar
- Center for Cardiovascular Genetics and Gene DiagnosticsFoundation for People with Rare DiseasesSchlieren‐ZurichSwitzerland
| | - Janine Meienberg
- Center for Cardiovascular Genetics and Gene DiagnosticsFoundation for People with Rare DiseasesSchlieren‐ZurichSwitzerland
| | - Marianne Rohrbach
- Division of Metabolism and Children's Research CenterUniversity Children's Hospital Zurich Eleonore FoundationZurichSwitzerland
| | - Beat Steinmann
- Division of Metabolism and Children's Research CenterUniversity Children's Hospital Zurich Eleonore FoundationZurichSwitzerland
| | - Gabor Matyas
- Center for Cardiovascular Genetics and Gene DiagnosticsFoundation for People with Rare DiseasesSchlieren‐ZurichSwitzerland
- Zurich Center for Integrative Human PhysiologyUniversity of ZurichZurichSwitzerland
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7
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Pu Z, Sun H, Du J, Cheng Y, He K, Ni B, Gu W, Dai J, Shao Y. Family-based whole-exome sequencing identifies novel loss-of-function mutations of FBN1 for Marfan syndrome. PeerJ 2018; 6:e5927. [PMID: 30479897 PMCID: PMC6238762 DOI: 10.7717/peerj.5927] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/13/2018] [Indexed: 12/30/2022] Open
Abstract
Background Marfan syndrome (MFS) is an inherited connective tissue disorder affecting the ocular, skeletal and cardiovascular systems. Previous studies of MFS have demonstrated the association between genetic defects and clinical manifestations. Our purpose was to investigate the role of novel genetic variants in determining MFS clinical phenotypes. Methods We sequenced the whole exome of 19 individuals derived from three Han Chinese families. The sequencing data were analyzed by a standard pipeline. Variants were further filtered against the public database and an in-house database. Then, we performed pedigree analysis under different inheritance patterns according to American College of Medical Genetics guidelines. Results were confirmed by Sanger sequencing. Results Two novel loss-of-function indels (c.5027_5028insTGTCCTCC, p.D1677Vfs*8; c.5856delG, p.S1953Lfs*27) and one nonsense variant (c.8034C>A, p.Y2678*) of FBN1 were identified in Family 1, Family 2 and Family 3, respectively. All affected members carried pathogenic mutations, whereas other unaffected family members or control individuals did not. These different kinds of loss of function (LOF) variants of FBN1 were located in the cbEGF region and a conserved domain across species and were not reported previously. Conclusions Our study extended and strengthened the vital role of FBN1 LOF mutations in the pathogenesis of MFS with an autosomal dominant inheritance pattern. We confirm that genetic testing by next-generation sequencing of blood DNA can be fundamental in helping clinicians conduct mutation-based pre- and postnatal screening, genetic diagnosis and clinical management for MFS.
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Affiliation(s)
- Zhening Pu
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China.,Center of Clinical Research, Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China
| | - Haoliang Sun
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Junjie Du
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yue Cheng
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Keshuai He
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Buqing Ni
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Weidong Gu
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Juncheng Dai
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Yongfeng Shao
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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8
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Takeda N, Inuzuka R, Morita H, Komuro I. Response by Takeda et al to Letter Regarding Article, “Impact of Pathogenic FBN1Variant Types on the Progression of Aortic Disease in Patients With Marfan Syndrome”. Circ Genom Precis Med 2018; 11:e002321. [DOI: 10.1161/circgen.118.002321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Norifumi Takeda
- Department of Cardiovascular Medicine, The University of Tokyo Hospital, Japan (N.T., H.M., I.K.)
| | - Ryo Inuzuka
- Department of Pediatrics (R.I.), The University of Tokyo Hospital, Japan
| | - Hiroyuki Morita
- Department of Cardiovascular Medicine, The University of Tokyo Hospital, Japan (N.T., H.M., I.K.)
| | - Issei Komuro
- Department of Cardiovascular Medicine, The University of Tokyo Hospital, Japan (N.T., H.M., I.K.)
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9
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Overwater E, Marsili L, Baars MJH, Baas AF, van de Beek I, Dulfer E, van Hagen JM, Hilhorst-Hofstee Y, Kempers M, Krapels IP, Menke LA, Verhagen JMA, Yeung KK, Zwijnenburg PJG, Groenink M, van Rijn P, Weiss MM, Voorhoeve E, van Tintelen JP, Houweling AC, Maugeri A. Results of next-generation sequencing gene panel diagnostics including copy-number variation analysis in 810 patients suspected of heritable thoracic aortic disorders. Hum Mutat 2018; 39:1173-1192. [PMID: 29907982 PMCID: PMC6175145 DOI: 10.1002/humu.23565] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 05/23/2018] [Accepted: 05/30/2018] [Indexed: 01/02/2023]
Abstract
Simultaneous analysis of multiple genes using next-generation sequencing (NGS) technology has become widely available. Copy-number variations (CNVs) in disease-associated genes have emerged as a cause for several hereditary disorders. CNVs are, however, not routinely detected using NGS analysis. The aim of this study was to assess the diagnostic yield and the prevalence of CNVs using our panel of Hereditary Thoracic Aortic Disease (H-TAD)-associated genes. Eight hundred ten patients suspected of H-TAD were analyzed by targeted NGS analysis of 21 H-TAD associated genes. In addition, the eXome hidden Markov model (XHMM; an algorithm to identify CNVs in targeted NGS data) was used to detect CNVs in these genes. A pathogenic or likely pathogenic variant was found in 66 of 810 patients (8.1%). Of these 66 pathogenic or likely pathogenic variants, six (9.1%) were CNVs not detectable by routine NGS analysis. These CNVs were four intragenic (multi-)exon deletions in MYLK, TGFB2, SMAD3, and PRKG1, respectively. In addition, a large duplication including NOTCH1 and a large deletion encompassing SCARF2 were detected. As confirmed by additional analyses, both CNVs indicated larger chromosomal abnormalities, which could explain the phenotype in both patients. Given the clinical relevance of the identification of a genetic cause, CNV analysis using a method such as XHMM should be incorporated into the clinical diagnostic care for H-TAD patients.
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Affiliation(s)
- Eline Overwater
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands.,Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Luisa Marsili
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands.,Medical Genetics Unit, Tor Vergata University Hospital, Rome, Italy
| | - Marieke J H Baars
- Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Annette F Baas
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Irma van de Beek
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands.,Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Eelco Dulfer
- Department of Genetics, University Medical Center Groningen, Groningen, the Netherlands
| | - Johanna M van Hagen
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | | | - Marlies Kempers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Ingrid P Krapels
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Leonie A Menke
- Department of Pediatrics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Judith M A Verhagen
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Kak K Yeung
- Department of Surgery, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, the Netherlands.,Department of Physiology, Institute for Cardiovascular Research, VU University Medical Center, Amsterdam, the Netherlands
| | - Petra J G Zwijnenburg
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - Maarten Groenink
- Department of Cardiology and Radiology, Academic Medical Center Amsterdam, University of Amsterdam, Amsterdam, the Netherlands
| | - Peter van Rijn
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - Marjan M Weiss
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - Els Voorhoeve
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - J Peter van Tintelen
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands.,Department of Clinical Genetics, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Arjan C Houweling
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
| | - Alessandra Maugeri
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, the Netherlands
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10
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Chen M, Yao B, Yang Q, Deng J, Song Y, Sui T, Zhou L, Yao H, Xu Y, Ouyang H, Pang D, Li Z, Lai L. Truncated C-terminus of fibrillin-1 induces Marfanoid-progeroid-lipodystrophy (MPL) syndrome in rabbit. Dis Model Mech 2018; 11:dmm.031542. [PMID: 29666143 PMCID: PMC5963856 DOI: 10.1242/dmm.031542] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 03/05/2018] [Indexed: 12/12/2022] Open
Abstract
Various clinical differences have been observed between patients with the FBN1 gene mutation and those with the classical Marfan phenotype. Although FBN1 knockout (KO) or dominant-negative mutant mice are widely used as an animal model for Marfan syndrome (MFS), these mice cannot recapitulate the genotype/phenotype relationship of Marfanoid-progeroid-lipodystrophy (MPL) syndrome, which is caused by a mutation in the C-terminus of fibrillin-1, the penultimate exon of the FBN1 gene. Here, we describe the generation of a rabbit MPL model with C-terminal truncation of fibrillin-1 using a CRISPR/Cas9 system. FBN1 heterozygous (FBN1 Het) rabbits faithfully recapitulated the phenotypes of MFS, including muscle wasting and impaired connective tissue, ocular syndrome and aortic dilation. Moreover, skin symptoms, lipodystrophy, growth retardation and dysglycemia were also seen in these FBN1 Het rabbits, and have not been reported in other animal models. In conclusion, this novel rabbit model mimics the histopathological changes and functional defects of MPL syndrome, and could become a valuable model for studies of pathogenesis and drug screening for MPL syndrome. Summary: A novel genetically engineered rabbit model of MPL syndrome, generated by CRISPR/Cas9-mediated mutation of FBN1, mimics the histopathological changes and functional defects of MPL syndrome seen in the clinic.
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Affiliation(s)
- Mao Chen
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Bing Yao
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Qiangbing Yang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Jichao Deng
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Yuning Song
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Tingting Sui
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Lina Zhou
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - HaoBing Yao
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Yuanyuan Xu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Hongsheng Ouyang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Daxin Pang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Zhanjun Li
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China
| | - Liangxue Lai
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, Jilin University, Changchun 130062, China .,Key Laboratory of Regenerative Biology, Chinese Academy of Sciences, and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530, China
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11
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Benke K, Ágg B, Meienberg J, Kopps AM, Fattorini N, Stengl R, Daradics N, Pólos M, Bors A, Radovits T, Merkely B, De Backer J, Szabolcs Z, Mátyás G. Hungarian Marfan family with large FBN1 deletion calls attention to copy number variation detection in the current NGS era. J Thorac Dis 2018; 10:2456-2460. [PMID: 29850152 DOI: 10.21037/jtd.2018.04.40] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Copy number variations (CNVs) comprise about 10% of reported disease-causing mutations in Mendelian disorders. Nevertheless, pathogenic CNVs may have been under-detected due to the lack or insufficient use of appropriate detection methods. In this report, on the example of the diagnostic odyssey of a patient with Marfan syndrome (MFS) harboring a hitherto unreported 32-kb FBN1 deletion, we highlight the need for and the feasibility of testing for CNVs (>1 kb) in Mendelian disorders in the current next-generation sequencing (NGS) era.
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Affiliation(s)
- Kálmán Benke
- Heart and Vascular Center, Semmelweis University, Budapest, Hungary.,Hungarian Marfan Foundation, Budapest, Hungary
| | - Bence Ágg
- Heart and Vascular Center, Semmelweis University, Budapest, Hungary.,Hungarian Marfan Foundation, Budapest, Hungary.,Department of Pharmacology and Pharmacotherapy, Semmelweis University, Budapest, Hungary
| | - Janine Meienberg
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - Anna M Kopps
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - Nathalie Fattorini
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - Roland Stengl
- Heart and Vascular Center, Semmelweis University, Budapest, Hungary.,Hungarian Marfan Foundation, Budapest, Hungary
| | - Noémi Daradics
- Heart and Vascular Center, Semmelweis University, Budapest, Hungary.,Hungarian Marfan Foundation, Budapest, Hungary
| | - Miklós Pólos
- Heart and Vascular Center, Semmelweis University, Budapest, Hungary.,Hungarian Marfan Foundation, Budapest, Hungary
| | - András Bors
- Laboratory of Molecular Diagnostics, Hungarian National Blood Transfusion Service, Budapest, Hungary
| | - Tamás Radovits
- Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Béla Merkely
- Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Julie De Backer
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Zoltán Szabolcs
- Heart and Vascular Center, Semmelweis University, Budapest, Hungary.,Hungarian Marfan Foundation, Budapest, Hungary
| | - Gábor Mátyás
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
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12
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Analysis of 31-year-old patient with SYNGAP1 gene defect points to importance of variants in broader splice regions and reveals developmental trajectory of SYNGAP1-associated phenotype: case report. BMC MEDICAL GENETICS 2017; 18:62. [PMID: 28576131 PMCID: PMC5457574 DOI: 10.1186/s12881-017-0425-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/22/2017] [Indexed: 12/21/2022]
Abstract
Background Whole exome sequencing is a powerful tool for the analysis of genetically heterogeneous conditions. The prioritization of variants identified often focuses on nonsense, frameshift and canonical splice site mutations, and highly deleterious missense variants, although other defects can also play a role. The definition of the phenotype range and course of rare genetic conditions requires long-term clinical follow-up of patients. Case presentation We report an adult female patient with severe intellectual disability, severe speech delay, epilepsy, autistic features, aggressiveness, sleep problems, broad-based clumsy gait and constipation. Whole exome sequencing identified a de novo mutation in the SYNGAP1 gene. The variant was located in the broader splice donor region of intron 10 and replaced G by A at position +5 of the splice site. The variant was predicted in silico and shown experimentally to abolish the regular splice site and to activate a cryptic donor site within exon 10, causing frameshift and premature termination. The overall clinical picture of the patient corresponded well with the characteristic SYNGAP1-associated phenotype observed in previously reported patients. However, our patient was 31 years old which contrasted with most other published SYNGAP1 cases who were much younger. Our patient had a significant growth delay and microcephaly. Both features normalised later, although the head circumference stayed only slightly above the lower limit of the norm. The patient had a delayed puberty. Her cognitive and language performance remained at the level of a one-year-old child even in adulthood and showed a slow decline. Myopathic facial features and facial dysmorphism became more pronounced with age. Although the gait of the patient was unsteady in childhood, more severe gait problems developed in her teens. While the seizures remained well-controlled, her aggressive behaviour worsened with age and required extensive medication. Conclusions The finding in our patient underscores the notion that the interpretation of variants identified using whole exome sequencing should focus not only on variants in the canonical splice dinucleotides GT and AG, but also on broader splice regions. The long-term clinical follow-up of our patient contributes to the knowledge of the developmental trajectory in individuals with SYNGAP1 gene defects. Electronic supplementary material The online version of this article (doi:10.1186/s12881-017-0425-4) contains supplementary material, which is available to authorized users.
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13
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Näf E, Laubscher D, Hopfer H, Streit M, Matyas G. Birt-Hogg-Dubé syndrome: novel FLCN frameshift deletion in daughter and father with renal cell carcinomas. Fam Cancer 2016; 15:127-32. [PMID: 26342594 PMCID: PMC4698292 DOI: 10.1007/s10689-015-9837-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Germline mutation of the FLCN gene causes Birt–Hogg–Dubé syndrome (BHD), a rare autosomal dominant condition characterized by skin fibrofolliculomas, lung cysts, spontaneous pneumothorax and renal tumours. We identified a hitherto unreported pathogenic FLCN frameshift deletion c.563delT (p.Phe188Serfs*35) in a family of a 46-year-old woman presented with macrohematuria due to bilateral chromophobe renal carcinomas. A heritable renal cancer was suspected due to the bilaterality of the tumour and as the father of this woman had suffered from renal cancer. Initially, however, BHD was overlooked by the medical team despite the highly suggestive clinical presentation. We assume that BHD is underdiagnosed, at least partially, due to low awareness of this variable condition and to insufficient use of appropriate genetic testing. Our study indicates that BHD and FLCN testing should be routinely considered in patients with positive family or personal history of renal tumours. In addition, we demonstrate how patients and their families can play a driving role in initiating genetic diagnosis, presymptomatic testing of at-risk relatives, targeted disease management, and genetic counselling of rare diseases such as BHD.
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Affiliation(s)
- Ernst Näf
- Department of Practice Development in Nursing, Solothurner Spitäler AG, Olten, Switzerland
| | - Dominik Laubscher
- Genetic Center of the Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - Helmut Hopfer
- Institute for Pathology, University Hospital, Basel, Switzerland
| | - Markus Streit
- Department of Dermatology, Kantonsspital, Aarau, Switzerland
| | - Gabor Matyas
- Genetic Center of the Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland. .,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland.
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14
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Jameel M, Klar J, Tariq M, Moawia A, Altaf Malik N, Seema Waseem S, Abdullah U, Naeem Khan T, Raininko R, Baig SM, Dahl N. A novel AP4M1 mutation in autosomal recessive cerebral palsy syndrome and clinical expansion of AP-4 deficiency. BMC MEDICAL GENETICS 2014; 15:133. [PMID: 25496299 PMCID: PMC4292821 DOI: 10.1186/s12881-014-0133-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 12/03/2014] [Indexed: 11/21/2022]
Abstract
Background Cerebral palsy (CP) is a heterogeneous neurodevelopmental disorder associated with intellectual disability in one-third of cases. Recent findings support Mendelian inheritance in subgroups of patients with the disease. The purpose of this study was to identify a novel genetic cause of paraplegic CP with intellectual disability in a consanguineous Pakistani family. Methods We performed whole-exome sequencing (WES) in two brothers with CP and intellectual disability. Analysis of AP4M1 mRNA was performed using quantitative real-time PCR on total RNA from cultured fibroblasts. The brothers were investigated clinically and by MRI. Results We identified a novel homozygous AP4M1 mutation c.194_195delAT, p.Y65Ffs*50 in the affected brothers. Quantitative RT-PCR analysis showed markedly reduced AP4M1 mRNA levels suggesting partial non-sense mediated mRNA decay. Several clinical and MRI features were consistent with AP-4 complex deficiency. However, in contrast to previously reported cases with AP4M1 mutations our patients show an aggressive behavior and a relatively late onset of disease. Conclusion This study shows an AP4M1 mutation associated with aggressive behavior in addition to mild dysmorphic features, intellectual disability, spastic paraparesis and reduced head circumference. Our findings expand the clinical spectrum associated with AP-4 complex deficiency and the study illustrates the importance of MRI and WES in the diagnosis of patients with CP and intellectual disability.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala 751 08, Sweden.
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15
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Franken R, Heesterbeek TJ, de Waard V, Zwinderman AH, Pals G, Mulder BJM, Groenink M. Diagnosis and genetics of Marfan syndrome. Expert Opin Orphan Drugs 2014. [DOI: 10.1517/21678707.2014.950223] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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16
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Musova Z, Kaiserova M, Kriegova E, Fillerova R, Vasovcak P, Santava A, Mensikova K, Zumrova A, Krepelova A, Sedlacek Z, Kanovsky P. A Novel Frameshift Mutation in the AFG3L2 Gene in a Patient with Spinocerebellar Ataxia. THE CEREBELLUM 2013; 13:331-7. [DOI: 10.1007/s12311-013-0538-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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17
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Cawley NX, Wetsel WC, Murthy SRK, Park JJ, Pacak K, Loh YP. New roles of carboxypeptidase E in endocrine and neural function and cancer. Endocr Rev 2012; 33:216-53. [PMID: 22402194 PMCID: PMC3365851 DOI: 10.1210/er.2011-1039] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 01/18/2012] [Indexed: 01/14/2023]
Abstract
Carboxypeptidase E (CPE) or carboxypeptidase H was first discovered in 1982 as an enkephalin-convertase that cleaved a C-terminal basic residue from enkephalin precursors to generate enkephalin. Since then, CPE has been shown to be a multifunctional protein that subserves many essential nonenzymatic roles in the endocrine and nervous systems. Here, we review the phylogeny, structure, and function of CPE in hormone and neuropeptide sorting and vesicle transport for secretion, alternative splicing of the CPE transcript, and single nucleotide polymorphisms in humans. With this and the analysis of mutant and knockout mice, the data collectively support important roles for CPE in the modulation of metabolic and glucose homeostasis, bone remodeling, obesity, fertility, neuroprotection, stress, sexual behavior, mood and emotional responses, learning, and memory. Recently, a splice variant form of CPE has been found to be an inducer of tumor growth and metastasis and a prognostic biomarker for metastasis in endocrine and nonendocrine tumors.
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Affiliation(s)
- Niamh X Cawley
- Section on Cellular Neurobiology, Program on Developmental Neuroscience, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
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18
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Sorte H, Mørkrid L, Rødningen O, Kulseth MA, Stray-Pedersen A, Matthijs G, Race V, Houge G, Fiskerstrand T, Bjurulf B, Lyle R, Prescott T. Severe ALG8-CDG (CDG-Ih) associated with homozygosity for two novel missense mutations detected by exome sequencing of candidate genes. Eur J Med Genet 2012; 55:196-202. [PMID: 22306853 DOI: 10.1016/j.ejmg.2012.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2011] [Accepted: 01/08/2012] [Indexed: 02/08/2023]
Abstract
Posttranslationally glycosylated proteins are important in many biological processes in humans and Congenital disorders of glycosylation (CDGs) are associated with a broad range of phenotypes. Type I CDGs are a group of rare autosomal recessive conditions. To date 17 subtypes have been enzymatically and molecularly characterized. Impaired function of the enzyme dolichyl pyrophosphate Glc(1)Man(9)GlcNAc(2) alpha-1,3-glucosyltransferase encoded by the ALG8 gene, causes ALG8-CDG (CDG-Ih, OMIM #608104). This enzyme facilitates the transfer of a second glucose molecule to a growing lipid-linked oligosaccharide chain, a process that transpires in the endoplasmic reticulum (ER). We present a female patient of consanguineous parents, with pre- and postnatal growth retardation, dysmorphic features, significant developmental delay, visual impairment and an electrophoretic serum transferrin pattern indicative of a type I CDG. Type I CDG subgroup was determined by exome sequencing facilitated by homozygosity analysis. The patient was homozygous for two variants, nine nucleotides apart, in exon 8 of ALG8; c.799T > C [p.Ser267Pro] and c.808T > C [p.Phe270Leu]. Both missense mutations are predicted to affect a conserved region of an intraluminal ER loop of dolichyl pyrophosphate Glc(1)Man(9)GlcNAc(2) alpha-1,3-glucosyltransferase. To our knowledge, the current report describes the ninth published case of ALG8-CDG, contributing to the further delineation of this rare and variable disorder.
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Affiliation(s)
- Hanne Sorte
- Department of Medical Genetics, Oslo University Hospital, Nydalen, Oslo, Norway
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19
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Robinson DO, Lin F, Lyon M, Raponi M, Cross E, White HE, Cox H, Clayton-Smith J, Baralle D. Systematic screening of FBN1 gene unclassified missense variants for splice abnormalities. Clin Genet 2011; 82:223-31. [PMID: 21895641 DOI: 10.1111/j.1399-0004.2011.01781.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Defects at the level of pre-mRNA splicing are a common source of genetic mutation but such mutations are not always easy to identify from DNA sequence data alone. Clinical practice has only recently begun to incorporate analysis for this type of abnormality. Some base changes at the DNA level currently viewed as unclassified variants or missense mutations may influence RNA splicing. To address this problem for fibrillin 1 (FBN1) gene missense mutations we have carried out RNA analysis and in silico analysis with splice site prediction programs on 40 cases with 36 different mutations. Direct analysis of RNA from blood was performed by cDNA preparation, PCR amplification of specific FBN1 fragments, gel electrophoresis and sequencing of the PCR products. Of the 36 missense base changes, direct RNA analysis identified 2 which caused an abnormality of splicing. In silico analysis using five splice site prediction programs did not always accurately predict the splicing seen by direct RNA analysis. In conclusion, some apparent missense mutations have an effect on splicing which can be identified by direct RNA analysis, however, in silico analysis of splice sites is not always accurate, should be carried out with more than one prediction program and results should be used with caution.
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Affiliation(s)
- D O Robinson
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury, Wiltshire SP2 8BJ, UK.
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20
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Papp J, Kovacs ME, Solyom S, Kasler M, Børresen-Dale AL, Olah E. High prevalence of germline STK11 mutations in Hungarian Peutz-Jeghers Syndrome patients. BMC MEDICAL GENETICS 2010; 11:169. [PMID: 21118512 PMCID: PMC3012662 DOI: 10.1186/1471-2350-11-169] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Accepted: 11/30/2010] [Indexed: 02/07/2023]
Abstract
BACKGROUND Peutz-Jeghers syndrome (PJS) is a rare autosomal dominantly inherited disease characterized by gastrointestinal hamartomatous polyposis and mucocutaneous pigmentation. The genetic predisposition for PJS has been shown to be associated with germline mutations in the STK11/LKB1 tumor suppressor gene. The aim of the present study was to characterize Hungarian PJS patients with respect to germline mutation in STK11/LKB1 and their association to disease phenotype. METHODS Mutation screening of 21 patients from 13 PJS families were performed using direct DNA sequencing and multiplex ligation-dependent probe amplification (MLPA). Comparative semi-quantitative sequencing was applied to investigate the mRNA-level effects of nonsense and splice-affecting mutations. RESULTS Thirteen different pathogenic mutations in STK11, including a high frequency of large genomic deletions (38%, 5/13), were identified in the 13 unrelated families studied. One of these deletions also affects two neighboring genes (SBNO2 and GPX4), located upstream of STK11, with a possible modifier effect. The majority of the point mutations (88%, 7/8) can be considered novel. Quantification of the STK11 transcript at the mRNA-level revealed that the expression of alleles carrying a nonsense or frameshift mutation was reduced to 30-70% of that of the wild type allele. Mutations affecting splice-sites around exon 2 displayed an mRNA processing pattern indicative of co-regulated splicing of exons 2 and 3. CONCLUSIONS A combination of sensitive techniques may assure a high (100%) STK11 mutation detection frequency in PJS families. Characterization of mutations at mRNA level may give a deeper insight into the molecular consequences of the pathogenic mutations than predictions made solely at the genomic level.
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Affiliation(s)
- Janos Papp
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Marietta Eva Kovacs
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Szilvia Solyom
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
- Laboratory of Cancer Genetics, Department of Clinical Genetics and Biocenter Oulu, University of Oulu, Oulu University Hospital, Oulu, Finland
| | - Miklos Kasler
- Department of Head and Neck Surgery, National Institute of Oncology, Budapest, Hungary
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute for Clinical Medicine, Faculty of Medicine, Univeristy of Oslo, Norway
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
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Zuercher J, Neidhardt J, Magyar I, Labs S, Moore AT, Tanner FC, Waseem N, Schorderet DF, Munier FL, Bhattacharya S, Berger W, Kloeckener-Gruissem B. Alterations of the 5'untranslated region of SLC16A12 lead to age-related cataract. Invest Ophthalmol Vis Sci 2010; 51:3354-61. [PMID: 20181839 PMCID: PMC2904002 DOI: 10.1167/iovs.10-5193] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Revised: 02/04/2010] [Accepted: 02/09/2010] [Indexed: 11/24/2022] Open
Abstract
PURPOSE. Knowledge of genetic factors predisposing to age-related cataract is very limited. The aim of this study was to identify DNA sequences that either lead to or predispose for this disease. METHODS. The candidate gene SLC16A12, which encodes a solute carrier of the monocarboxylate transporter family, was sequenced in 484 patients with cataract (134 with juvenile cataract, 350 with age-related cataract) and 190 control subjects. Expression studies included luciferase reporter assay and RT-PCR experiments. RESULTS. One patient with age-related cataract showed a novel heterozygous mutation (c.-17A>G) in the 5'untranslated region (5'UTR). This mutation is in cis with the minor G-allele of the single nucleotide polymorphism (SNP) rs3740030 (c.-42T/G), also within the 5'UTR. Using a luciferase reporter assay system, a construct with the patient's haplotype caused a significant upregulation of luciferase activity. In comparison, the SNP G-allele alone promoted less activity, but that amount was still significantly higher than the amount of the common T-allele. Analysis of SLC16A12 transcripts in surrogate tissue demonstrated striking allele-specific differences causing 5'UTR heterogeneity with respect to sequence and quantity. These differences in gene expression were mirrored in an allele-specific predisposition to age-related cataract, as determined in a Swiss population (odds ratio approximately 2.2; confidence intervals, 1.23-4.3). CONCLUSIONS. The monocarboxylate transporter SLC16A12 may contribute to age-related cataract. Sequences within the 5'UTR modulate translational efficiency with pathogenic consequences.
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Affiliation(s)
- Jurian Zuercher
- From the Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - John Neidhardt
- From the Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Istvan Magyar
- From the Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Stephan Labs
- From the Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Anthony T. Moore
- Moorfields Eye Hospital London, London, United Kingdom
- UCL-Institute of Ophthalmology, London, United Kingdom
| | - Felix C. Tanner
- the Department of Cardiology, Cardiovascular Center, University of Zurich, Zurich, Switzerland
| | | | - Daniel F. Schorderet
- IRO-Institute for Research in Ophthalmology, EPFL-École polytechnique fédérale of Lausanne and University of Lausanne, Lausanne, Switzerland
| | - Francis L. Munier
- Jules Gonin Eye Hospital, Faculté de Biologie et Médecine de L'Université de Lausanne, Switzerland; and
| | | | - Wolfgang Berger
- From the Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Barbara Kloeckener-Gruissem
- From the Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
- the Department of Biology, ETH Zurich, Zurich, Switzerland
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