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Peeters MHCA, Khan M, Rooijakkers AAMB, Mulders T, Haer-Wigman L, Boon CJF, Klaver CCW, van den Born LI, Hoyng CB, Cremers FPM, den Hollander AI, Dhaenens CM, Collin RWJ. PRPH2 mutation update: In silico assessment of 245 reported and 7 novel variants in patients with retinal disease. Hum Mutat 2021; 42:1521-1547. [PMID: 34411390 PMCID: PMC9290825 DOI: 10.1002/humu.24275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/22/2021] [Accepted: 08/16/2021] [Indexed: 01/31/2023]
Abstract
Mutations in PRPH2, encoding peripherin-2, are associated with the development of a wide variety of inherited retinal diseases (IRDs). To determine the causality of the many PRPH2 variants that have been discovered over the last decades, we surveyed all published PRPH2 variants up to July 2020, describing 720 index patients that in total carried 245 unique variants. In addition, we identified seven novel PRPH2 variants in eight additional index patients. The pathogenicity of all variants was determined using the ACMG guidelines. With this, 107 variants were classified as pathogenic, 92 as likely pathogenic, one as benign, and two as likely benign. The remaining 50 variants were classified as variants of uncertain significance. Interestingly, of the total 252 PRPH2 variants, more than half (n = 137) were missense variants. All variants were uploaded into the Leiden Open source Variation and ClinVar databases. Our study underscores the need for experimental assays for variants of unknown significance to improve pathogenicity classification, which would allow us to better understand genotype-phenotype correlations, and in the long-term, hopefully also support the development of therapeutic strategies for patients with PRPH2-associated IRD.
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Affiliation(s)
- Manon H C A Peeters
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Mubeen Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | | | - Timo Mulders
- Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Camiel J F Boon
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Ophthalmology, Amsterdam UMC, Academic Medical Center, Amsterdam, The Netherlands
| | - Caroline C W Klaver
- Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Ophthalmology, Erasmus University Medical Centre, Rotterdam, The Netherlands.,Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
| | - L Ingeborgh van den Born
- The Rotterdam Eye Hospital, Rotterdam, The Netherlands.,Rotterdam Ophthalmic Institute, Rotterdam, The Netherlands
| | - Carel B Hoyng
- Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Anneke I den Hollander
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Claire-Marie Dhaenens
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Biochemistry and Molecular Biology, Univ. Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, Lille, France
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
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2
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Lasa-Fernandez H, Mosqueira-Martín L, Alzualde A, Lasa-Elgarresta J, Vallejo-Illarramendi A. A genotyping method combining primer competition PCR with HRM analysis to identify point mutations in Duchenne animal models. Sci Rep 2020; 10:17224. [PMID: 33057138 PMCID: PMC7560699 DOI: 10.1038/s41598-020-74173-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/28/2020] [Indexed: 11/09/2022] Open
Abstract
Dystrophin-null sapje zebrafish is an excellent model for better understanding the pathological mechanisms underlying Duchenne muscular dystrophy, and it has recently arisen as a powerful tool for high-throughput screening of therapeutic candidates for this disease. While dystrophic phenotype in sapje larvae can be easily detected by birefringence, zebrafish genotyping is necessary for drug screening experiments, where the potential rescue of larvae phenotype is the primary outcome. Genotyping is also desirable during colony husbandry since heterozygous progenitors need to be selected. Currently, sapje zebrafish are genotyped through techniques involving sequencing or multi-step PCR, which are often costly, tedious, or require special equipment. Here we report a simple, precise, cost-effective, and versatile PCR genotyping method based on primer competition. Genotypes can be resolved by standard agarose gel electrophoresis and high-resolution melt assay, the latter being especially useful for genotyping a large number of samples. Our approach has shown high sensitivity, specificity, and reproducibility in detecting the A/T point mutation in sapje zebrafish and the C/T mutation in the mdx mouse model of Duchenne. Hence, this method can be applied to other single nucleotide substitutions and may be further optimized to detect small insertions and deletions. Given its robust performance with crude DNA extracts, our strategy may be particularly well-suited for detecting single nucleotide variants in poor-quality samples such as ancient DNA or DNA from formalin-fixed, paraffin-embedded material.
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Affiliation(s)
- Haizpea Lasa-Fernandez
- Group of Neurosciences, Dept. Pediatrics, University of the Basque Country UPV/EHU, Hospital Universitario Donostia, Paseo Dr. Begiristain 105, 20014, San Sebastián, Spain
- Group of Neuromuscular Diseases, Biodonostia Health Research Institute, Paseo Dr. Begiristain s/n, 20014, San Sebastián, Spain
- CIBERNED, Instituto de Salud Carlos III, 28031, Madrid, Spain
| | - Laura Mosqueira-Martín
- Group of Neurosciences, Dept. Pediatrics, University of the Basque Country UPV/EHU, Hospital Universitario Donostia, Paseo Dr. Begiristain 105, 20014, San Sebastián, Spain
- Group of Neuromuscular Diseases, Biodonostia Health Research Institute, Paseo Dr. Begiristain s/n, 20014, San Sebastián, Spain
- CIBERNED, Instituto de Salud Carlos III, 28031, Madrid, Spain
| | | | - Jaione Lasa-Elgarresta
- Group of Neurosciences, Dept. Pediatrics, University of the Basque Country UPV/EHU, Hospital Universitario Donostia, Paseo Dr. Begiristain 105, 20014, San Sebastián, Spain
- Group of Neuromuscular Diseases, Biodonostia Health Research Institute, Paseo Dr. Begiristain s/n, 20014, San Sebastián, Spain
- CIBERNED, Instituto de Salud Carlos III, 28031, Madrid, Spain
| | - Ainara Vallejo-Illarramendi
- Group of Neurosciences, Dept. Pediatrics, University of the Basque Country UPV/EHU, Hospital Universitario Donostia, Paseo Dr. Begiristain 105, 20014, San Sebastián, Spain.
- Group of Neuromuscular Diseases, Biodonostia Health Research Institute, Paseo Dr. Begiristain s/n, 20014, San Sebastián, Spain.
- CIBERNED, Instituto de Salud Carlos III, 28031, Madrid, Spain.
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3
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Yak FOXO1 and FOXO3 SNPs and association with production traits, and their promotes cells apoptosis via RNAi. Gene 2020; 743:144592. [PMID: 32198125 DOI: 10.1016/j.gene.2020.144592] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
FOXOs transcription factors not only play key roles in glucose metabolism, muscle atrophy and energy homeostasis but also play crucial transcriptional regulatory roles in the cell's metabolism, orchestrating programs of gene expression that regulate cell apoptosis, cell-cycle progression and oxidative stress resistance. However, the specific function of FOXOs promoting fibroblasts proliferation and apoptosis are still unknown. Thus, we used the High-Resolution Melting (HRM) and RNA interference methods to detect SNPs and function. We found one SNP in the exon of FOXO1, three SNPs were identified in the exon of FOXO3, and three SNPs and production traits were significantly different. The siRNA sequence of yak FOXO1 and FOXO3 were transfected into the yak fibroblasts, and effects were detected by a series of assays to reveal the function in yak fibroblasts. The results demonstrated that down-regulated expression of FOXO1 and FOXO3 resulted in up-regulated the expression of BAX, Caspase9 and Caspase3, and down-regulated the expression level of anti-apoptotic gene of BCL2. The apoptotic situation was consistent with results of the flow cytometry and Tunel test cell cycle and cell vitality results revealed that knockdown FOXO1 and FOXO3 resulted in increased P27 expression level and decreased CyclinD1. Meanwhile, cell vitality was also decreased. These results demonstrated that FOXO1 and FOXO3 are two novel regulatory factors to suppress cells proliferation and promote cells apoptosis. Furthermore, these results provide evidence that FOXO1 and FOXO3 play a functional role in cell apoptosis.
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Wang Q, Zhang Q, Wang X, Zhang Y, Zhao X. WITHDRAWN: Yak FOXO1 and FOXO3 SNPs and association with production traits, and their promotes cells apoptosis via RNAi. Gene X 2020. [DOI: 10.1016/j.gene.2020.100029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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5
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Zhang Y, Shi F, Yu Z, Yang A, Zeng M, Wang J, Yin H, Zhang B, Ma X. A cross-sectional study on factors associated with hypertension and genetic polymorphisms of renin-angiotensin-aldosterone system in Chinese hui pilgrims to hajj. BMC Public Health 2019; 19:1223. [PMID: 31484569 PMCID: PMC6727391 DOI: 10.1186/s12889-019-7357-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/22/2019] [Indexed: 01/11/2023] Open
Abstract
Background Hypertension is the leading risk factor for cardiovascular disease (CVD), however, the studies on lifestyle and genetic risks in Chinese pilgrims to Hajj was limited. The aim of this study is to examine the prevalence and associated lifestyle and genetic risks for hypertension among Hui Hajj pilgrims in China. Methods We performed a cross-sectional analysis of data in 1,465 participants aged 30–70 years who participated in a medical examination for Hui Hajj pilgrims from Gansu province, China in 2017. Multiple logistic regression was used to evaluate the association of potential risk factors with hypertension. Deoxyribonucleic acid (DNA) polymorphism was examined at sites in the renin-angiotensin-aldosterone system (RAAS). Results The prevalence of hypertension was 47% among this population. Lifestyle factors such as fried food preference (like vs. dislike: odds ratio [OR]: =1.53, 95% confidence interval [CI]: 1.13–2.09) and barbecued food preference (like vs. dislike: OR = 1.45, 95% CI: 1.06–1.97) were associated with elevated risk of hypertension among Hui pilgrims. Comparing with Angiotensin converting enzyme (ACE) rs4425 AA genotype, TT genotype was associated with hypertension risk (OR = 2.16, 95% CI: 1.17–4.00). Similar results were also observed for ACE rs4437 CC genotype (OR = 1.95, 95% CI: 1.07–3.55), Angiotensin II receptor (ATR) rs129876 AA genotype (OR = 4.10, 95% CI: 2.30–7.32) and Aldosterone synthase (CYP11B2) rs1912 TT genotype (OR = 2.82, 95% CI: 1.57–5.06) genotypes. Conclusions Unhealthy lifestyle and genetic factors were associated with the prevalence of hypertension in Chinese Hui pilgrims and their interactions were also observed. Electronic supplementary material The online version of this article (10.1186/s12889-019-7357-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yinxia Zhang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610000, China.,Northwest Minzu University, Lanzhou, 730030, China
| | - Fangfang Shi
- Center for Disease Control and Prevention, Kongtong District, Pingliang, Gansu, China
| | - Zhanbiao Yu
- Qingyang People's Hospital, Qingyang, 745000, China
| | - Aimin Yang
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Kowloon, Hong Kong SAR
| | - Maolan Zeng
- Northwest Minzu University, Lanzhou, 730030, China
| | - Jiaoyue Wang
- Gansu International Travel Healthcare Center, Lanzhou, 730000, China
| | - Haiping Yin
- Gansu International Travel Healthcare Center, Lanzhou, 730000, China
| | - Benzhong Zhang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Xiao Ma
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, 610000, China.
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6
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A new approach based on targeted pooled DNA sequencing identifies novel mutations in patients with Inherited Retinal Dystrophies. Sci Rep 2018; 8:15457. [PMID: 30337596 PMCID: PMC6194132 DOI: 10.1038/s41598-018-33810-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 10/04/2018] [Indexed: 01/28/2023] Open
Abstract
Inherited retinal diseases (IRD) are a heterogeneous group of diseases that mainly affect the retina; more than 250 genes have been linked to the disease and more than 20 different clinical phenotypes have been described. This heterogeneity both at the clinical and genetic levels complicates the identification of causative mutations. Therefore, a detailed genetic characterization is important for genetic counselling and decisions regarding treatment. In this study, we developed a method consisting on pooled targeted next generation sequencing (NGS) that we applied to 316 eye disease related genes, followed by High Resolution Melting and copy number variation analysis. DNA from 115 unrelated test samples was pooled and samples with known mutations were used as positive controls to assess the sensitivity of our approach. Causal mutations for IRDs were found in 36 patients achieving a detection rate of 31.3%. Overall, 49 likely causative mutations were identified in characterized patients, 14 of which were first described in this study (28.6%). Our study shows that this new approach is a cost-effective tool for detection of causative mutations in patients with inherited retinopathies.
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Ezquerra-Inchausti M, Barandika O, Anasagasti A, Irigoyen C, López de Munain A, Ruiz-Ederra J. High prevalence of mutations affecting the splicing process in a Spanish cohort with autosomal dominant retinitis pigmentosa. Sci Rep 2017; 7:39652. [PMID: 28045043 PMCID: PMC5206707 DOI: 10.1038/srep39652] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 11/24/2016] [Indexed: 01/24/2023] Open
Abstract
Retinitis pigmentosa is the most frequent group of inherited retinal dystrophies. It is highly heterogeneous, with more than 80 disease-causing genes 27 of which are known to cause autosomal dominant RP (adRP), having been identified. In this study a total of 29 index cases were ascertained based on a family tree compatible with adRP. A custom panel of 31 adRP genes was analysed by targeted next-generation sequencing using the Ion PGM platform in combination with Sanger sequencing. This allowed us to detect putative disease-causing mutations in 14 out of the 29 (48.28%) families analysed. Remarkably, around 38% of all adRP cases analysed showed mutations affecting the splicing process, mainly due to mutations in genes coding for spliceosome factors (SNRNP200 and PRPF8) but also due to splice-site mutations in RHO. Twelve of the 14 mutations found had been reported previously and two were novel mutations found in PRPF8 in two unrelated patients. In conclusion, our results will lead to more accurate genetic counselling and will contribute to a better characterisation of the disease. In addition, they may have a therapeutic impact in the future given the large number of studies currently underway based on targeted RNA splicing for therapeutic purposes.
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Affiliation(s)
| | - Olatz Barandika
- Division of Neurosciences, Biodonostia Health Research Institute, San Sebastián, Spain
| | - Ander Anasagasti
- Division of Neurosciences, Biodonostia Health Research Institute, San Sebastián, Spain
| | - Cristina Irigoyen
- Division of Neurosciences, Biodonostia Health Research Institute, San Sebastián, Spain.,Department of Ophthalmology, Donostia University Hospital, San Sebastián, Spain
| | - Adolfo López de Munain
- Division of Neurosciences, Biodonostia Health Research Institute, San Sebastián, Spain.,Department of Neurology, Donostia University Hospital, San Sebastián, Spain.,CIBERNED, Center for Networked Biomedical Research on Neurodegenerative Diseases, Institute of Health Carlos III, Ministry of Economy and Competitiveness, Spain.,Department of Neurosciences, University of the Basque Country UPV-EHU, Spain
| | - Javier Ruiz-Ederra
- Division of Neurosciences, Biodonostia Health Research Institute, San Sebastián, Spain
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8
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Barandika O, Irigoyen C, Anasagasti A, Egiguren G, Ezquerra-Inchausti M, López de Munain A, Ruiz-Ederra J. A Cost-Effective Mutation Screening Strategy for Inherited Retinal Dystrophies. Ophthalmic Res 2016; 56:123-31. [PMID: 27160245 DOI: 10.1159/000445690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/21/2016] [Indexed: 11/19/2022]
Abstract
OBJECTIVE We developed a simple, time- and cost-effective Excel-based genetic screening strategy for the diagnosis of inherited retinal dystrophies (IRD). DESIGN 76 patients diagnosed with IRD and 112 nonaffected family members, from 55 unrelated families, were included. DNA samples were analyzed using Axiom Exome Genotyping Array Plates (Affymetrix) that contain over 300,000 genetic variants, including more than 5,000 variants present in 181 genes involved in IRD. We used a simple Excel-based data mining strategy in order to screen IRD variants likely involved in the development of IRD. RESULTS A total of 5 relevant genetic variants were found in 5 IRD genes. Four variants were reported either as pathogenic or with a prediction of probably damaging, and 1 variant was reported to affect a regulatory region. These variants were present in 14 patients and in 11 carriers, in 10 unrelated families. CONCLUSION Using our Excel-based data screening strategy, we were able to assign likely genetic diagnoses in a fast and cost-effective manner to over 18% of patients analyzed, with a comparable ratio of genetic findings to that reported with retina-specific arrays for about 1/5 of the cost. Our approach proved efficient in reducing costs and time for IRD diagnosis as a first tier genetic screening method.
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Affiliation(s)
- Olatz Barandika
- Division of Neurosciences, Instituto Biodonostia, Donostia-San Sebastián, Spain
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9
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Identification of gene mutation in patients with osteogenesis imperfect using high resolution melting analysis. Sci Rep 2015; 5:13468. [PMID: 26307460 PMCID: PMC4549685 DOI: 10.1038/srep13468] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/28/2015] [Indexed: 11/08/2022] Open
Abstract
Osteogenesis imperfecta (OI), a congenital bone disorder, is caused by mutations in COL1A1 and COL1A2 genes, leading to deficiency of type I collagen. The high resolution melting (HRM) analysis has been used for detecting mutations, polymorphisms and epigenetic alteration in double-stranded DNAs. This study was to evaluate the potential application of HRM analysis for identifying gene mutations in patients with OI. This study included four children with OI and their parents and fifty normal people as controls. Blood samples were collected for HRM analysis of PCR-amplified exons and flanking DNA sequences of COL1A1 and COL1A2 genes. Direct gene sequencing was performed to validate HRM-identified gene mutations. As compared to controls, HRM analysis of samples form children with OI showed abnormal melting curves in exons 11 and 33–34 of the COL1A1 gene and exons 19 and 48 of the COL1A2 gene, which indicates the presence of heterozygous mutations in COL1A1 and COL1A2 genes. In addition to two known mutations in the COL1A2 gene, c.982G > A and c.3197G > T, sequencing analysis identified two novel mutations in the COL1A1 gene, c.2321delC and c.768dupC mutations, which function as premature stop codons. These results support future studies of applying HRM analysis as a diagnostic approach for OI.
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Nicchia E, Greco C, De Rocco D, Pecile V, D'Eustacchio A, Cappelli E, Corti P, Marra N, Ramenghi U, Pillon M, Farruggia P, Dufour C, Pallavicini A, Torelli L, Savoia A. Identification of point mutations and large intragenic deletions in Fanconi anemia using next-generation sequencing technology. Mol Genet Genomic Med 2015; 3:500-12. [PMID: 26740942 PMCID: PMC4694132 DOI: 10.1002/mgg3.160] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/22/2015] [Accepted: 05/27/2015] [Indexed: 12/30/2022] Open
Abstract
Fanconi anemia (FA) is a rare bone marrow failure disorder characterized by clinical and genetic heterogeneity with at least 17 genes involved, which make molecular diagnosis complex and time-consuming. Since next-generation sequencing technologies could greatly improve the genetic testing in FA, we sequenced DNA samples with known and unknown mutant alleles using the Ion PGM (™) system (IPGM). The molecular target of 74.2 kb in size covered 96% of the FA-coding exons and their flanking regions. Quality control testing revealed high coverage. Comparing the IPGM and Sanger sequencing output of FANCA,FANCC, and FANCG we found no false-positive and a few false-negative variants, which led to high sensitivity (95.58%) and specificity (100%) at least for these two most frequently mutated genes. The analysis also identified novel mutant alleles, including those in rare complementation groups FANCF and FANCL. Moreover, quantitative evaluation allowed us to characterize large intragenic deletions of FANCA and FANCD2, suggesting that IPGM is suitable for identification of not only point mutations but also copy number variations.
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Affiliation(s)
- Elena Nicchia
- Department of Medical Sciences University of Trieste Trieste Italy
| | - Chiara Greco
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo Trieste Italy
| | - Daniela De Rocco
- Department of Medical Sciences University of Trieste Trieste Italy
| | - Vanna Pecile
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo Trieste Italy
| | - Angela D'Eustacchio
- Institute for Maternal and Child Health - IRCCS Burlo Garofolo Trieste Italy
| | - Enrico Cappelli
- Clinical and Experimental Hematology Unit G. Gaslini Children's Hospital Genoa Italy
| | - Paola Corti
- Pediatrics Unit San Gerardo Hospital Monza Italy
| | - Nicoletta Marra
- Pediatric Hematology Unit Santobono Pausilipon Hospital Naples Italy
| | - Ugo Ramenghi
- Department of Pediatric and Public Health Sciences University of Torino Torino Italy
| | - Marta Pillon
- Pediatric Onco-Haematology Clinic University of Padua Padua Italy
| | - Piero Farruggia
- Pediatric Onco-Hematology ARNAS Civico Hospital Palermo Italy
| | - Carlo Dufour
- Clinical and Experimental Hematology Unit G. Gaslini Children's Hospital Genoa Italy
| | | | - Lucio Torelli
- Department of Mathematics and Geosciences University of Trieste Trieste Italy
| | - Anna Savoia
- Department of Medical SciencesUniversity of TriesteTriesteItaly; Institute for Maternal and Child Health - IRCCS Burlo GarofoloTriesteItaly
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11
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Zhou Q, Cheng J, Yang W, Tania M, Wang H, Khan MA, Duan C, Zhu L, Chen R, Lv H, Fu J. Identification of a novel heterozygous missense mutation in the CACNA1F gene in a chinese family with retinitis pigmentosa by next generation sequencing. BIOMED RESEARCH INTERNATIONAL 2015; 2015:907827. [PMID: 26075273 PMCID: PMC4449926 DOI: 10.1155/2015/907827] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Accepted: 09/14/2014] [Indexed: 12/18/2022]
Abstract
BACKGROUND Retinitis pigmentosa (RP) is an inherited retinal degenerative disease, which is clinically and genetically heterogeneous, and the inheritance pattern is complex. In this study, we have intended to study the possible association of certain genes with X-linked RP (XLRP) in a Chinese family. METHODS A Chinese family with RP was recruited, and a total of seven individuals were enrolled in this genetic study. Genomic DNA was isolated from peripheral leukocytes, and used for the next generation sequencing (NGS). RESULTS The affected individual presented the clinical signs of XLRP. A heterozygous missense mutation (c.1555C>T, p.R519W) was identified by NGS in exon 13 of the CACNA1F gene on X chromosome, and was confirmed by Sanger sequencing. It showed perfect cosegregation with the disease in the family. The mutation at this position in the CACNA1F gene of RP was found novel by database searching. CONCLUSION By using NGS, we have found a novel heterozygous missense mutation (c.1555C>T, p.R519W) in CACNA1F gene, which is probably associated with XLRP. The findings might provide new insights into the cause and diagnosis of RP, and have implications for genetic counseling and clinical management in this family.
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Affiliation(s)
- Qi Zhou
- Department of Ophthalmology, Affiliated Hospital of Luzhou Medical College, Luzhou, Sichuan 646000, China
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Luzhou Medical College, Luzhou, Sichuan 646000, China
| | - Jingliang Cheng
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Luzhou Medical College, Luzhou, Sichuan 646000, China
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Weichan Yang
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Luzhou Medical College, Luzhou, Sichuan 646000, China
| | - Mousumi Tania
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Luzhou Medical College, Luzhou, Sichuan 646000, China
| | - Hui Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Md. Asaduzzaman Khan
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Luzhou Medical College, Luzhou, Sichuan 646000, China
| | - Chengxia Duan
- Department of Ophthalmology, Affiliated Hospital of Luzhou Medical College, Luzhou, Sichuan 646000, China
| | - Li Zhu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Luzhou Medical College, Luzhou, Sichuan 646000, China
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hongbin Lv
- Department of Ophthalmology, Affiliated Hospital of Luzhou Medical College, Luzhou, Sichuan 646000, China
| | - Junjiang Fu
- Key Laboratory of Epigenetics and Oncology, The Research Center for Preclinical Medicine, Luzhou Medical College, Luzhou, Sichuan 646000, China
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12
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Zhao L, Wang F, Wang H, Li Y, Alexander S, Wang K, Willoughby CE, Zaneveld JE, Jiang L, Soens ZT, Earle P, Simpson D, Silvestri G, Chen R. Next-generation sequencing-based molecular diagnosis of 82 retinitis pigmentosa probands from Northern Ireland. Hum Genet 2014; 134:217-30. [PMID: 25472526 DOI: 10.1007/s00439-014-1512-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/20/2014] [Indexed: 11/24/2022]
Abstract
Retinitis pigmentosa (RP) is a group of inherited retinal disorders characterized by progressive photoreceptor degeneration. An accurate molecular diagnosis is essential for disease characterization and clinical prognoses. A retinal capture panel that enriches 186 known retinal disease genes, including 55 known RP genes, was developed. Targeted next-generation sequencing was performed for a cohort of 82 unrelated RP cases from Northern Ireland, including 46 simplex cases and 36 familial cases. Disease-causing mutations were identified in 49 probands, including 28 simplex cases and 21 familial cases, achieving a solving rate of 60 %. In total, 65 pathogenic mutations were found, and 29 of these were novel. Interestingly, the molecular information of 12 probands was neither consistent with their initial inheritance pattern nor clinical diagnosis. Further clinical reassessment resulted in a refinement of the clinical diagnosis in 11 patients. This is the first study to apply next-generation sequencing-based, comprehensive molecular diagnoses to a large number of RP probands from Northern Ireland. Our study shows that molecular information can aid clinical diagnosis, potentially changing treatment options, current family counseling and management.
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Affiliation(s)
- Li Zhao
- Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
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Massó JFM, Zarranz JJ, Otaegui D, López de Munain A. Neurogenetic Disorders in the Basque Population. Ann Hum Genet 2014; 79:57-75. [DOI: 10.1111/ahg.12088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 09/11/2014] [Indexed: 12/12/2022]
Affiliation(s)
- José Félix Martí Massó
- Department of Neurology at Hospital Universitario Donostia (San Sebastián, Guipúzcoa); Basque Health Service (Osakidetza); Basque Country Spain
- Department of Neurosciences; University of Basque Country (UPV-EHU)
- Centre for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED); Carlos III Health Institute, Ministry of Economy and Competitiveness; Spain
- BioDonostia Institute, San Sebastián, Guipúzcoa
- JAKIUNDE, Academia de las Ciencias, de las Artes y de las Letras
| | - Juan José Zarranz
- Department of Neurology at Hospital Universitario Cruces (Baracaldo, Vizcaya); Basque Health Service (Osakidetza); Basque Country Spain
- Department of Neurosciences; University of Basque Country (UPV-EHU)
- BioCruces Institute, Baracaldo; Vizcaya
- JAKIUNDE, Academia de las Ciencias, de las Artes y de las Letras
| | | | - Adolfo López de Munain
- Department of Neurology at Hospital Universitario Donostia (San Sebastián, Guipúzcoa); Basque Health Service (Osakidetza); Basque Country Spain
- Department of Neurosciences; University of Basque Country (UPV-EHU)
- Centre for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED); Carlos III Health Institute, Ministry of Economy and Competitiveness; Spain
- BioDonostia Institute, San Sebastián, Guipúzcoa
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