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Bhardwaj A, Yadav A, Yadav M, Tanwar M. Genetic dissection of non-syndromic retinitis pigmentosa. Indian J Ophthalmol 2022; 70:2355-2385. [PMID: 35791117 PMCID: PMC9426071 DOI: 10.4103/ijo.ijo_46_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Retinitis pigmentosa (RP) belongs to a group of pigmentary retinopathies. It is the most common form of inherited retinal dystrophy, characterized by progressive degradation of photoreceptors that leads to nyctalopia, and ultimately, complete vision loss. RP is distinguished by the continuous retinal degeneration that progresses from the mid-periphery to the central and peripheral retina. RP was first described and named by Franciscus Cornelius Donders in the year 1857. It is one of the leading causes of bilateral blindness in adults, with an incidence of 1 in 3000 people worldwide. In this review, we are going to focus on the genetic heterogeneity of this disease, which is provided by various inheritance patterns, numerosity of variations and inter-/intra-familial variations based upon penetrance and expressivity. Although over 90 genes have been identified in RP patients, the genetic cause of approximately 50% of RP cases remains unknown. Heterogeneity of RP makes it an extremely complicated ocular impairment. It is so complicated that it is known as “fever of unknown origin”. For prognosis and proper management of the disease, it is necessary to understand its genetic heterogeneity so that each phenotype related to the various genetic variations could be treated.
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Affiliation(s)
- Aarti Bhardwaj
- Department of Genetics, M. D. University, Rohtak, Haryana, India
| | - Anshu Yadav
- Department of Genetics, M. D. University, Rohtak, Haryana, India
| | - Manoj Yadav
- Department of Genetics, M. D. University, Rohtak, Haryana, India
| | - Mukesh Tanwar
- Department of Genetics, M. D. University, Rohtak, Haryana, India
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2
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Ng TK, Cao Y, Yuan XL, Chen S, Xu Y, Chen SL, Zheng Y, Chen H. Whole exome sequencing analysis identifies novel Stargardt disease-related gene mutations in Chinese Stargardt disease and retinitis pigmentosa patients. Eye (Lond) 2022; 36:749-759. [PMID: 33846575 PMCID: PMC8956586 DOI: 10.1038/s41433-021-01525-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/17/2021] [Accepted: 03/29/2021] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES To delineate the disease-causing mutations of the Stargardt disease-related genes in Chinese patients diagnosed with Stargardt disease or retinitis pigmentosa (RP) by whole exome sequencing analysis. METHODS A total of 123 sporadic RP or Stargardt disease patients and 2 Stargardt disease families were recruited. All sporadic patients and the probands of the families were subjected to whole exome sequencing analysis. The candidate mutations were verified by direct sequencing based on the cosegregation pattern and in 200 control subjects and by the bioinformatics analyses. RESULTS A total of three reported ABCA4 mutations were identified in the probands of the two Stargardt disease families. The probands and the affected family members with either homozygous or compound heterozygous mutations showed typical Stargardt disease features, which was absent in their unaffected family members. The cosegregation pattern confirmed the mode of recessive inheritance. Moreover, two sporadic Stargardt disease patients were identified to carry two novel ABCA4 and one PROM1 mutations. In addition, 13 novel variants were found in 119 sporadic RP patients in 7 Stargardt disease-related genes, and 8 novel missense variants were conserved across different species and predicted to be damaging to the protein. All 15 novel variants were absent in our 200 control subjects. CONCLUSIONS This study revealed 22.4% study subjects carrying Stargardt disease-related gene mutations with total 15 novel variants in seven Stargardt disease-related genes, assuring that targeted next-generation sequencing analysis is a high throughput strategy to facilitate the clinical diagnosis from suspicious patients and recommended as a routine examination for inherited retinal dystrophies.
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Affiliation(s)
- Tsz Kin Ng
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
- Shantou University Medical College, Shantou, Guangdong, China
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yingjie Cao
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Xiang-Ling Yuan
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
- Shantou University Medical College, Shantou, Guangdong, China
| | - Shaowan Chen
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Yanxuan Xu
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Shao-Lang Chen
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Yuqian Zheng
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
| | - Haoyu Chen
- Joint Shantou International Eye Center of Shantou University and The Chinese University of Hong Kong, Shantou, Guangdong, China
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3
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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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4
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Mermeklieva E, Kamenarova K, Mihova K, Shakola F, Kaneva R. A rare case of RGR/CDHR1 haplotype identified in Bulgarian patient with cone-rod dystrophy. Ophthalmic Genet 2021; 42:747-752. [PMID: 34229535 DOI: 10.1080/13816810.2021.1946700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
AIM To present a rare clinical case of CDHR1-related retinopathy with cone and rod involvementconfirmed clinically, electrophysiologically and genetically as a cone-rod dystrophy. MATERIAL AND METHODS A 26-year-old woman underwent detailed ophthalmic examinationincluding fundus photography, full-field and multifocal electroretinography, visual field testing, optical coherence tomography and fluorescein angiography, which established the clinical diagnosis. Next-generation sequencing of a custom panel including 140 of the most common genes for inherited retinal degenerations was used for mutation screening. RESULTS The symptoms onset was two years ago included gradual loss of vision and photophobia. The clinical findings were reduced visual acuity, central and peripheral scotomas, sporadic pigmentary cells localized mainly in the peripheral retina, a thinner retina in the macula and peripherally, moderate retinal vessels attenuation and reduced cone and rod ERG responses. The genetic analysisfound that the patient was homozygous for two already reported mutations: RGR-c.196A>C (p.Ser66Arg) variant and a co-segregating frame-shift deletion in CDHR1-c.2522_2528delTCTCTGA (p.Ile841Serfs119*). Segregation analysis showed that the two mutations were transmitted by the asymptomatic heterozygous parents. CONCLUSION The rare haplotype of RGR mutation co-segregating incis- with CDHR1 mutation in our patient has been previously described in Albanian patients with recessive retinal dystrophy. Our findings add further support to the hypothesis of a common ancestral haplotype spread in the Balkan population. The comprehensive clinical, electrophysiological and genetic testing of patients with rare hereditary retinal dystrophies is essential for the correct diagnosis and the choice of potential novel therapies.
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Affiliation(s)
- Elena Mermeklieva
- Clinic of Оphthalmology, "Lozenetz" University Hospital, Medical Faculty, Sofia University "St. Kliment Ohridski", Sofia, Bulgaria
| | - Kunka Kamenarova
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
| | - Kalina Mihova
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
| | - Felitsiya Shakola
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
| | - Radka Kaneva
- Molecular Medicine Center, Department of Medical Chemistry and Biochemistry, Medical Faculty, Medical University - Sofia, Sofia, Bulgaria
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Falfoul Y, Matri KE, Habibi I, Halouani S, Chebil A, Schorderet D, El Matri L. OCT-angiography assessing quiescent and active choroidal neovascularization in retinitis pigmentosa associated with PRPH2 pathogenic variant. Eur J Ophthalmol 2021; 32:NP98-NP102. [PMID: 33736480 DOI: 10.1177/11206721211004396] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE To report multimodal imaging findings including optical coherence tomography angiography (OCT-A) of a patient presenting with a quiescent choroidal neovascularization (CNV) in one eye and an active CNV in the fellow eye, complicating retinitis pigmentosa (RP) linked to PRPH2 pathogenic variant, with follow-up and management of both eyes. METHODS Observational case report. RESULTS A 40-year-old female with history of autosomal dominant RP consulted for acute visual loss in her right eye (RE). Multimodal imaging including OCT-A confirmed the diagnosis of active type 2 CNV in the RE and highlighted an incidental asymptomatic non-exudative "quiescent" CNV in the left eye (LE). This complication was managed by intra-vitreal Bevacizumab injections in the RE and regular monitoring of the LE. Frequent follow-up could detect early CNV activation signs in LE allowing early treatment. Mutation analysis of PRPH2 exons identified a known heterozygous pathogenic missense variation c.646C>T, p.P216S in exon 2. CONCLUSION Multimodal imaging and especially OCT-A can be of a great help in the diagnosis and the management of CNV complicating RP, even at the stage of quiescent CNV. In presence of neovascular complication, PRPH2 gene should be investigated because of its frequent macular involvement despite high phenotypic variability.
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Affiliation(s)
- Yousra Falfoul
- Department B, Institut Hédi Raies d'ophtalmologie de Tunis, Tunis, Tunisia.,Oculogenetic Laboratory LR14SP01, Tunis, Tunisia.,Faculté de Médecine de Tunis, Université de Tunis - El Manar, Tunis, Tunisia
| | - Khaled El Matri
- Department B, Institut Hédi Raies d'ophtalmologie de Tunis, Tunis, Tunisia.,Oculogenetic Laboratory LR14SP01, Tunis, Tunisia.,Faculté de Médecine de Tunis, Université de Tunis - El Manar, Tunis, Tunisia
| | - Imen Habibi
- Institut de Recherche en Ophtalmologie, Sion, Switzerland
| | - Safa Halouani
- Department B, Institut Hédi Raies d'ophtalmologie de Tunis, Tunis, Tunisia.,Faculté de Médecine de Tunis, Université de Tunis - El Manar, Tunis, Tunisia
| | - Ahmed Chebil
- Department B, Institut Hédi Raies d'ophtalmologie de Tunis, Tunis, Tunisia.,Oculogenetic Laboratory LR14SP01, Tunis, Tunisia.,Faculté de Médecine de Tunis, Université de Tunis - El Manar, Tunis, Tunisia
| | - Daniel Schorderet
- Institut de Recherche en Ophtalmologie, Sion, Switzerland.,Faculté de Biologie et de Médecine, Université de Lausanne, Lausanne, Switzerland.,Faculté des Sciences de la Vie, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Leila El Matri
- Department B, Institut Hédi Raies d'ophtalmologie de Tunis, Tunis, Tunisia.,Oculogenetic Laboratory LR14SP01, Tunis, Tunisia.,Faculté de Médecine de Tunis, Université de Tunis - El Manar, Tunis, Tunisia
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6
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Nebbioso M, Franzone F, Lambiase A, La Cava M, Mallone F, Pizzuti A, Marchionni E. X-linked dominant RPGR gene mutation in a familial Coats angiomatosis. BMC Ophthalmol 2021; 21:37. [PMID: 33446141 PMCID: PMC7807486 DOI: 10.1186/s12886-020-01791-5] [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: 05/13/2020] [Accepted: 12/25/2020] [Indexed: 11/15/2022] Open
Abstract
Background Retinitis Pigmentosa (RP) is the most frequent retinal hereditary disease and every kind of transmission pattern has been described. The genetic etiology of RP is extremely heterogeneous and in the last few years the large application of Next Generation Sequencing (NGS) approaches improved the diagnostic yield, elucidating previously unexplained RP causes and new genotype-phenotype correlations. The objective of this study was to reevaluate a previously reported family affected by Coats’-type RP without genetic diagnosis and to describe the new genetic findings. Case presentation Cohort, prospective, and single-center observational family case. Three individuals of a family, consisting of a mother and four sons, with a Coats phenotype were revaluated after 25 years of clinical follow-up using visual acuity tests, ophthalmoscopy, Goldmann visual field, electroretinography (ERG), and spectral domain-optical coherence tomography (SD-OCT). Specifically, a RP NGS panel was performed on one member of the family and segregation analysis was required for the other affected and unaffected members. NGS analysis disclosed a RPGR (Retinitis Pigmentosa GTPase Regulator) gene truncating variant segregating with the phenotype in all the three affected members. RPGR mutations are reported as causative of an X-linked RP. Conclusions This is the first reported family with a Coats’-type RP associated to a RPGR mutation and segregating as a dominant X-linked disease, confirming the hypothesis of the genetic origin of this condition and expanding the phenotypic spectrum of diseases caused by RPGR gene mutations. The Authors suggest RPGR gene screening mutations in patients presenting this phenotype.
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Affiliation(s)
- Marcella Nebbioso
- Department of Sense Organs, Faculty of Medicine and Odontology, Sapienza University of Rome, p. le A. Moro 5, 00185, Rome, Italy
| | - Federica Franzone
- Department of Sense Organs, Faculty of Medicine and Odontology, Sapienza University of Rome, p. le A. Moro 5, 00185, Rome, Italy
| | - Alessandro Lambiase
- Department of Sense Organs, Faculty of Medicine and Odontology, Sapienza University of Rome, p. le A. Moro 5, 00185, Rome, Italy. .,Department of Sense Organs, Sapienza University of Rome, Viale del Policlinico 155, 00161, Rome, Italy.
| | - Maurizio La Cava
- Department of Sense Organs, Faculty of Medicine and Odontology, Sapienza University of Rome, p. le A. Moro 5, 00185, Rome, Italy
| | - Fabiana Mallone
- Department of Sense Organs, Faculty of Medicine and Odontology, Sapienza University of Rome, p. le A. Moro 5, 00185, Rome, Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Faculty of Medicine and Odontology, Sapienza University of Rome, p. le A. Moro 5, 00185, Rome, Italy
| | - Enrica Marchionni
- Department of Experimental Medicine, Faculty of Medicine and Odontology, Sapienza University of Rome, p. le A. Moro 5, 00185, Rome, Italy
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7
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Ragazzo M, Carboni S, Caputo V, Buttini C, Manzo L, Errichiello V, Puleri G, Giardina E. Interpreting Mixture Profiles: Comparison between Precision ID GlobalFiler™ NGS STR Panel v2 and Traditional Methods. Genes (Basel) 2020; 11:E591. [PMID: 32466613 PMCID: PMC7349666 DOI: 10.3390/genes11060591] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 04/28/2020] [Accepted: 05/22/2020] [Indexed: 12/11/2022] Open
Abstract
Forensic investigation for the identification of offenders, recognition of human remains, and verification of family relationships requires the analysis of particular types of highly informative DNA markers, which have high discriminatory power and are efficient for typing degraded samples. These markers, called STRs (Short Tandem Repeats), can be amplified by multiplex-PCR (Polymerase Chain Reaction) allowing attainment of a unique profile through which it is possible to distinguish one individual from another with a high statistical significance. The rapid and progressive evolution of analytical techniques and the advent of Next-Generation Sequencing (NGS) have completely revolutionized the DNA sequencing approach. This technology, widely used today in the diagnostic field, has the advantage of being able to process several samples in parallel, producing a huge volume of data in a short time. At this time, although default parameters of interpretation software are available, there is no general agreement on the interpretation rules of forensic data produced via NGS technology. Here we report a pilot study aimed for a comparison between NGS (Precision ID GlobalFiler™ NGS STR Panel v2, Thermo Fisher Scientific, Waltham, MA, USA) and traditional methods in their ability to identify major and minor contributors in DNA mixtures from saliva and urine samples. A quantity of six mixed samples were prepared for both saliva and urine samples from donors. A total of 12 mixtures were obtained in the ratios of 1:2; 1:4; 1:6; 1:8; 1:10; and 1:20 between minor and major contributors. Although the number of analyzed mixtures is limited, our results confirm that NGS technology offers a huge range of additional information on samples, but cannot ensure a higher sensitivity in respect to traditional methods. Finally, the Precision ID GlobalFiler™ NGS STR Panel v2 is a powerful method for kinship analyses and typing reference samples, but its use in biological evidence should be carefully considered on the basis of the characteristics of the evidence.
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Affiliation(s)
- Michele Ragazzo
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (V.C.); (C.B.); (L.M.); (V.E.); (G.P.)
| | - Stefania Carboni
- Genomic Medicine Laboratory UILDM, Santa Lucia Foundation IRCCS, 00142 Rome, Italy;
| | - Valerio Caputo
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (V.C.); (C.B.); (L.M.); (V.E.); (G.P.)
| | - Carlotta Buttini
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (V.C.); (C.B.); (L.M.); (V.E.); (G.P.)
| | - Laura Manzo
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (V.C.); (C.B.); (L.M.); (V.E.); (G.P.)
| | - Valeria Errichiello
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (V.C.); (C.B.); (L.M.); (V.E.); (G.P.)
| | - Giulio Puleri
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (V.C.); (C.B.); (L.M.); (V.E.); (G.P.)
| | - Emiliano Giardina
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (V.C.); (C.B.); (L.M.); (V.E.); (G.P.)
- Genomic Medicine Laboratory UILDM, Santa Lucia Foundation IRCCS, 00142 Rome, Italy;
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8
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Ragazzo M, Melchiorri S, Manzo L, Errichiello V, Puleri G, Nicastro F, Giardina E. Comparative Analysis of ANDE 6C Rapid DNA Analysis System and Traditional Methods. Genes (Basel) 2020; 11:E582. [PMID: 32456006 PMCID: PMC7288309 DOI: 10.3390/genes11050582] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/10/2020] [Accepted: 05/20/2020] [Indexed: 12/25/2022] Open
Abstract
Rapid DNA analysis is an ultrafast and fully automated DNA-typing system, which can produce interpretable genetic profiles from biological samples within 90 minutes. This "swab in-profile out" method comprises DNA extraction, amplification by PCR multiplex, separation and detection of DNA fragments by capillary electrophoresis. The aim of study was the validation of the Accelerated Nuclear DNA Equipment (ANDE) 6C system as a typing method for reference samples according to the ISO/IEC 17025 standard. Here, we report the evaluation of the validity and reproducibility of results by the comparison of the genetic profiles generated by the ANDE 6C System with those generated by standard technologies. A quantity of 104 buccal swabs were analyzed both through the ANDE 6C technology and the traditional method (DNA extraction and quantification, amplification and separation by capillary electrophoresis). Positive typing was observed in 97% of cases for ANDE 6C technology with only three buccal swabs failing to reveal interpretable signals. Concordance was determined by comparing the allele calls generated by ANDE 6C and conventional technology. Comparison of 2800 genotypes revealed a concordance rate of 99.96%. These results met the ISO/IEC 17025 requirements, enabling us to receive the accreditation for this method. Finally, rapid technology has certainly reached a level of reliability which has made its use in laboratories of forensic genetics a reality.
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Affiliation(s)
- Michele Ragazzo
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (S.M.); (L.M.); (V.E.); (G.P.)
| | - Stefano Melchiorri
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (S.M.); (L.M.); (V.E.); (G.P.)
| | - Laura Manzo
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (S.M.); (L.M.); (V.E.); (G.P.)
| | - Valeria Errichiello
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (S.M.); (L.M.); (V.E.); (G.P.)
| | - Giulio Puleri
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (S.M.); (L.M.); (V.E.); (G.P.)
| | | | - Emiliano Giardina
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy; (M.R.); (S.M.); (L.M.); (V.E.); (G.P.)
- Genomic Medicine Laboratory UILDM, IRCCS Santa Lucia Foundation, 00179 Rome, Italy
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9
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Strafella C, Caputo V, Campoli G, Galota RM, Mela J, Zampatti S, Minozzi G, Sancricca C, Servidei S, Giardina E, Cascella R. Genetic Counseling and NGS Screening for Recessive LGMD2A Families. High Throughput 2020; 9:ht9020013. [PMID: 32397577 PMCID: PMC7349198 DOI: 10.3390/ht9020013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/18/2020] [Accepted: 05/06/2020] [Indexed: 12/20/2022] Open
Abstract
Genetic counseling applied to limb–girdle muscular dystrophies (LGMDs) can be very challenging due to their clinical and genetic heterogeneity and the availability of different molecular assays. Genetic counseling should therefore be addressed to select the most suitable approach to increase the diagnostic rate and provide an accurate estimation of recurrence risk. This is particularly true for families with a positive history for recessive LGMD, in which the presence of a known pathogenetic mutation segregating within the family may not be enough to exclude the risk of having affected children without exploring the genetic background of phenotypically unaffected partners. In this work, we presented a family with a positive history for LGMD2A (OMIM #253600, also known as calpainopathy) characterized by compound heterozygosity for two CAPN3 mutations. The genetic specialist suggested the segregation analysis of both mutations within the family as a first-level analysis. Sequentially, next-generation sequencing (NGS) analysis was performed in the partners of healthy carriers to provide an accurate recurrence/reproductive risk estimation considering the genetic background of the couple. Finally, this work highlighted the importance of providing a genetic counseling/testing service even in unaffected individuals with a carrier partner. This approach can support genetic counselors in estimating the reproductive/recurrence risk and eventually, suggesting prenatal testing, early diagnosis or other medical surveillance strategies.
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Affiliation(s)
- Claudia Strafella
- Genomic Medicine Laboratory UILDM, Santa Lucia Foundation, 00179 Rome, Italy; (V.C.); (G.C.); (R.M.G.); (J.M.); (S.Z.); (E.G.); (R.C.)
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy
- Correspondence:
| | - Valerio Caputo
- Genomic Medicine Laboratory UILDM, Santa Lucia Foundation, 00179 Rome, Italy; (V.C.); (G.C.); (R.M.G.); (J.M.); (S.Z.); (E.G.); (R.C.)
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy
| | - Giulia Campoli
- Genomic Medicine Laboratory UILDM, Santa Lucia Foundation, 00179 Rome, Italy; (V.C.); (G.C.); (R.M.G.); (J.M.); (S.Z.); (E.G.); (R.C.)
| | - Rosaria Maria Galota
- Genomic Medicine Laboratory UILDM, Santa Lucia Foundation, 00179 Rome, Italy; (V.C.); (G.C.); (R.M.G.); (J.M.); (S.Z.); (E.G.); (R.C.)
| | - Julia Mela
- Genomic Medicine Laboratory UILDM, Santa Lucia Foundation, 00179 Rome, Italy; (V.C.); (G.C.); (R.M.G.); (J.M.); (S.Z.); (E.G.); (R.C.)
| | - Stefania Zampatti
- Genomic Medicine Laboratory UILDM, Santa Lucia Foundation, 00179 Rome, Italy; (V.C.); (G.C.); (R.M.G.); (J.M.); (S.Z.); (E.G.); (R.C.)
| | - Giulietta Minozzi
- Department of Veterinary Medicine, University of Milan, 20133 Milan, Italy;
| | - Cristina Sancricca
- Fondazione Policlinico Universitario A. Gemelli IRCCS, UOC Neurofisiopatologia, 00168 Rome, Italy; (C.S.); (S.S.)
- Unione Italiana Lotta Distrofia Muscolare (UILDM), Sezione Laziale, 00167 Rome, Italy
| | - Serenella Servidei
- Fondazione Policlinico Universitario A. Gemelli IRCCS, UOC Neurofisiopatologia, 00168 Rome, Italy; (C.S.); (S.S.)
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDM, Santa Lucia Foundation, 00179 Rome, Italy; (V.C.); (G.C.); (R.M.G.); (J.M.); (S.Z.); (E.G.); (R.C.)
- Department of Biomedicine and Prevention, Tor Vergata University, 00133 Rome, Italy
| | - Raffaella Cascella
- Genomic Medicine Laboratory UILDM, Santa Lucia Foundation, 00179 Rome, Italy; (V.C.); (G.C.); (R.M.G.); (J.M.); (S.Z.); (E.G.); (R.C.)
- Department of Biomedical Sciences, Catholic University Our Lady of Good Counsel, 1000 Tirana, Albania
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