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Whelan L, Dockery A, Stephenson KAJ, Zhu J, Kopčić E, Post IJM, Khan M, Corradi Z, Wynne N, O' Byrne JJ, Duignan E, Silvestri G, Roosing S, Cremers FPM, Keegan DJ, Kenna PF, Farrar GJ. Detailed analysis of an enriched deep intronic ABCA4 variant in Irish Stargardt disease patients. Sci Rep 2023; 13:9380. [PMID: 37296172 PMCID: PMC10256698 DOI: 10.1038/s41598-023-35889-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Over 15% of probands in a large cohort of more than 1500 inherited retinal degeneration patients present with a clinical diagnosis of Stargardt disease (STGD1), a recessive form of macular dystrophy caused by biallelic variants in the ABCA4 gene. Participants were clinically examined and underwent either target capture sequencing of the exons and some pathogenic intronic regions of ABCA4, sequencing of the entire ABCA4 gene or whole genome sequencing. ABCA4 c.4539 + 2028C > T, p.[= ,Arg1514Leufs*36] is a pathogenic deep intronic variant that results in a retina-specific 345-nucleotide pseudoexon inclusion. Through analysis of the Irish STGD1 cohort, 25 individuals across 18 pedigrees harbour ABCA4 c.4539 + 2028C > T and another pathogenic variant. This includes, to the best of our knowledge, the only two homozygous patients identified to date. This provides important evidence of variant pathogenicity for this deep intronic variant, highlighting the value of homozygotes for variant interpretation. 15 other heterozygous incidents of this variant in patients have been reported globally, indicating significant enrichment in the Irish population. We provide detailed genetic and clinical characterization of these patients, illustrating that ABCA4 c.4539 + 2028C > T is a variant of mild to intermediate severity. These results have important implications for unresolved STGD1 patients globally with approximately 10% of the population in some western countries claiming Irish heritage. This study exemplifies that detection and characterization of founder variants is a diagnostic imperative.
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Affiliation(s)
- Laura Whelan
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland.
| | - Adrian Dockery
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
- Next Generation Sequencing Laboratory, Pathology Department, The Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - Kirk A J Stephenson
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin 2, Ireland
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - Julia Zhu
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - Ella Kopčić
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
| | - Iris J M Post
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
| | - Mubeen Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Language and Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- International Max Planck Research School for Language Sciences, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, and Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Niamh Wynne
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin 2, Ireland
| | - James J O' Byrne
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, Dublin 7, Ireland
- International Max Planck Research School for Language Sciences, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- National Centre for Inherited Metabolic Disorders, The Mater Misericordiae University Hospital, Dublin 7, Ireland
- School of Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Emma Duignan
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin 2, Ireland
| | - Giuliana Silvestri
- Centre for Experimental Medicine, Queen's University Belfast, Belfast, Northern Ireland, UK
- School of Medicine, University College Dublin, Dublin 4, Ireland
- Department of Ophthalmology, The Royal Victoria Hospital, Belfast, Northern Ireland, UK
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, and Maastricht University Medical Center+, Maastricht, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Academic Alliance Genetics, Radboud University Medical Center, Nijmegen, and Maastricht University Medical Center+, Maastricht, The Netherlands
| | - David J Keegan
- Mater Clinical Ophthalmic Genetics Unit, The Mater Misericordiae University Hospital, Dublin 7, Ireland
| | - Paul F Kenna
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin 2, Ireland
| | - G Jane Farrar
- The School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
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2
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Aziz N, Ullah M, Rashid A, Hussain Z, Shah K, Awan A, Khan M, Ullah I, Rehman AU. A novel homozygous missense substitution p.Thr313Ile in the PDE6B gene underlies autosomal recessive retinitis pigmentosa in a consanguineous Pakistani family. BMC Ophthalmol 2023; 23:116. [PMID: 36959549 PMCID: PMC10035148 DOI: 10.1186/s12886-023-02845-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 03/07/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Retinitis pigmentosa (RP) is one of the most frequent hereditary retinal diseases that often starts with night blindness and eventually leads to legal blindness. Our study aimed to identify the underlying genetic cause of autosomal recessive retinitis pigmentosa (arRP) in a consanguineous Pakistani family. METHODS Following a detailed ophthalmological examination of the patients by an ophthalmologist, whole-exome sequencing was performed on the proband's DNA to delineate the genetic cause of RP in the family. In-depth computational methods, in-silico analysis, and familial co-segregation study were performed for variant detection and validation. RESULTS We studied an inbred Pakistani family with two siblings affected by retinitis pigmentosa. The proband, a 32 years old female, was clinically diagnosed with RP at the age of 6 years. A classical night blindness symptom was reported in the proband since her early childhood. OCT report showed a major reduction in the outer nuclear layer and the ellipsoid zone width, leading to the progression of the disease. Exome sequencing revealed a novel homozygous missense mutation (c.938C > T;p.Thr313Ile) in exon 12 of the PDE6B gene. The mutation p.Thr313Ile co-segregated with RP phenotype in the family. The altered residue (p.Thr313) was super conserved evolutionarily across different vertebrate species, and all available in silico tools classified the mutation as highly pathogenic. CONCLUSION We present a novel homozygous pathogenic mutation in the PDE6B gene as the underlying cause of arRP in a consanguineous Pakistani family. Our findings highlight the importance of missense mutations in the PDE6B gene and expand the known mutational repertoire of PDE6B-related RP.
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Affiliation(s)
- Nobia Aziz
- Department of Biotechnology and Genetic Engineering, Faculty of Biological and Health Sciences, Hazara University, Mansehra, Pakistan
| | - Mukhtar Ullah
- Institute of Molecular and Clinical Ophthalmology Basel, University of Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Abdur Rashid
- Department of Higher Education Archives and Libraries Peshawar, Government of Khyber Pakhtunkhwa, Peshawar, Pakistan
| | - Zubair Hussain
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
| | - Khadim Shah
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, Pakistan
| | - Azeem Awan
- LRBT Secondary Eye Hospital, Reerah Galla, Balakot Road, Mansehra, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Khan
- Department of Biotechnology and Genetic Engineering, Faculty of Biological and Health Sciences, Hazara University, Mansehra, Pakistan
| | - Inam Ullah
- Department of Biotechnology and Genetic Engineering, Faculty of Biological and Health Sciences, Hazara University, Mansehra, Pakistan
| | - Atta Ur Rehman
- Department of Zoology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, Pakistan.
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3
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Tehreem R, Chen I, Shah MR, Li Y, Khan MA, Afshan K, Chen R, Firasat S. Exome Sequencing Identified Molecular Determinants of Retinal Dystrophies in Nine Consanguineous Pakistani Families. Genes (Basel) 2022; 13:genes13091630. [PMID: 36140798 PMCID: PMC9498396 DOI: 10.3390/genes13091630] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Inherited retinal dystrophies (IRDs) are a heterogeneous group of degenerative disorders of the retina. Retinitis Pigmentosa (RP) is a common type of IRD that causes night blindness and loss of peripheral vision and may progress to blindness. Mutations in more than 300 genes have been associated with syndromic and non-syndromic IRDs. Recessive forms are more frequent in populations where endogamy is a social preference, such as Pakistan. The aim of this study was to identify molecular determinants of IRDs with the common presentation of night blindness in consanguineous Pakistani families. This study included nine consanguineous IRD-affected families that presented autosomal recessive inheritance of the night blindness phenotype. DNA was extracted from blood samples. Targeted exome sequencing of 344 known genes for retinal dystrophies was performed. Screening of nine affected families revealed two novel (c.5571_5576delinsCTAGATand c.471dup in EYS and SPATA7 genes, respectively) and six reported pathogenic mutations (c.304C>A, c.187C>T, c.1560C>A, c.547C>T, c.109del and c.9911_11550del in PDE6A, USH2A, USH2A, NMNAT1, PAX6 and ALMS1 genes, respectively) segregating with disease phenotype in each respective family. Molecular determinants of hereditary retinal dystrophies were identified in all screened families. Identification of novel variants aid future diagnosis of retinal dystrophies and help to provide genetic counseling to affected families.
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Affiliation(s)
- Raeesa Tehreem
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, University Road, Islamabad 45320, Pakistan
| | - Iris Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mudassar Raza Shah
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, University Road, Islamabad 45320, Pakistan
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muzammil Ahmad Khan
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29111, Pakistan
- Department of Human Genetics, Sidra Medicine, Doha P.O. Box 26999, Qatar
| | - Kiran Afshan
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, University Road, Islamabad 45320, Pakistan
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence: (R.C.); (S.F.); Tel.: +(713)-798-5194 (R.C.); +92-51-9064-4410 (S.F.)
| | - Sabika Firasat
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, University Road, Islamabad 45320, Pakistan
- Correspondence: (R.C.); (S.F.); Tel.: +(713)-798-5194 (R.C.); +92-51-9064-4410 (S.F.)
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Sanseverino PB, Hoffmann A, Machado S, Farias M, Michels MS, Sanseverino MTV, Marostica PJC. High-risk twin pregnancy: case report of an adolescent patient with cystic fibrosis and systemic lupus erythematosus. J Med Case Rep 2022; 16:230. [PMID: 35641986 PMCID: PMC9153143 DOI: 10.1186/s13256-022-03399-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/01/2022] [Indexed: 12/04/2022] Open
Abstract
Background We present the first case to our knowledge of a spontaneous twin pregnancy in a 16-year-old Caucasian patient with cystic fibrosis and systemic lupus erythematosus. Cystic fibrosis is one of the most common autosomal recessive genetic disorders and primarily affects the respiratory and digestive systems. Systemic lupus erythematosus is a chronic inflammatory disease of unknown cause that affects nearly every organ. Patients with cystic fibrosis or systemic lupus erythematosus are progressively having longer life expectancy and better quality of life, which has led a greater number of female patients reporting the desire to become mothers. Case presentation We present a case of a Caucasian 16-year-old pregnant with twins being treated for both cystic fibrosis and systemic lupus erythematosus. She has two CFTR mutations: p.F508del and 1812_1G>A. In the second trimester, she was admitted for possible preterm labor, which was successfully stopped. The patient’s nutritional status worsened, and she had a pulmonary exacerbation as well as a flare of systemic lupus erythematosus. At the 28th gestational week, she presented with a massive hemoptysis episode. The cesarean delivery had no complications, and there were no serious immediate postpartum complications. Discussion and conclusions While adolescent pregnancies in and of themselves are considered high risk for both the young mothers and their children, they are further complicated when the mother has two chronic diseases and a twin pregnancy. We achieved positive results using a multidisciplinary approach; however, the risks involved were so high that major efforts are to be taken by our medical community to prevent unplanned pregnancies in all patients with cystic fibrosis, especially when a serious comorbidity like the one in this case is present.
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Affiliation(s)
- Paula Baptista Sanseverino
- Universidade Federal do Rio Grande do Sul-PPG Saúde da Criança e do Adolescente, Ramiro Barcelos 2400 /sala 220, Atanásio Belmonte 515/502, Porto Alegre, RS, 90520550, Brazil.
| | - Anneliese Hoffmann
- Hospital de Clínicas de Porto Alegre, Ramiro Barcelos 2350 /sala 1131, Porto Alegre, Brazil
| | - Sandra Machado
- Hospital de Clínicas de Porto Alegre, Ramiro Barcelos 2350, Porto Alegre, Brazil
| | - Mariana Farias
- Universidade Federal do Rio Grande do Sul-PPG Saúde da Criança e do Adolescente, Ramiro Barcelos 2400 /sala 220, Atanásio Belmonte 515/502, Porto Alegre, RS, 90520550, Brazil
| | - Marcus Silva Michels
- Universidade Federal do Rio Grande do Sul-Serviço de Genética HCPA, Ramiro Barcelos 2350, Porto Alegre, Brazil
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Rehman AU, Sepahi N, Bedoni N, Ravesh Z, Salmaninejad A, Cancellieri F, Peter VG, Quinodoz M, Mojarrad M, Pasdar A, Asad AG, Ghalamkari S, Piran M, Piran M, Superti-Furga A, Rivolta C. Whole exome sequencing in 17 consanguineous Iranian pedigrees expands the mutational spectrum of inherited retinal dystrophies. Sci Rep 2021; 11:19332. [PMID: 34588515 PMCID: PMC8481312 DOI: 10.1038/s41598-021-98677-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 09/06/2021] [Indexed: 11/24/2022] Open
Abstract
Inherited retinal dystrophies (IRDs) constitute one of the most heterogeneous groups of Mendelian human disorders. Using autozygome-guided next-generation sequencing methods in 17 consanguineous pedigrees of Iranian descent with isolated or syndromic IRD, we identified 17 distinct genomic variants in 11 previously-reported disease genes. Consistent with a recessive inheritance pattern, as suggested by pedigrees, variants discovered in our study were exclusively bi-allelic and mostly in a homozygous state (in 15 families out of 17, or 88%). Out of the 17 variants identified, 5 (29%) were never reported before. Interestingly, two mutations (GUCY2D:c.564dup, p.Ala189ArgfsTer130 and TULP1:c.1199G > A, p.Arg400Gln) were also identified in four separate pedigrees (two pedigrees each). In addition to expanding the mutational spectrum of IRDs, our findings confirm that the traditional practice of endogamy in the Iranian population is a prime cause for the appearance of IRDs.
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Affiliation(s)
- Atta Ur Rehman
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Neda Sepahi
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Nicola Bedoni
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Zeinab Ravesh
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Arash Salmaninejad
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Virginie G Peter
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Institute of Experimental Pathology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Mathieu Quinodoz
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Majid Mojarrad
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Pasdar
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Division of Applied Medicine, Medical School, University of Aberdeen, Aberdeen, UK
| | - Ali Ghanbari Asad
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | | | - Mehran Piran
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Mehrdad Piran
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Carlo Rivolta
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK. .,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland. .,Department of Ophthalmology, University of Basel, Basel, Switzerland.
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Homozygosity mapping coupled with whole-exome sequencing and protein modelling identified a novel missense mutation in GUCY2D in a consanguineous Pakistani family with Leber congenital amaurosis. J Genet 2021. [DOI: 10.1007/s12041-021-01310-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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7
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Next-Generation Sequencing Applications for Inherited Retinal Diseases. Int J Mol Sci 2021; 22:ijms22115684. [PMID: 34073611 PMCID: PMC8198572 DOI: 10.3390/ijms22115684] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 12/12/2022] Open
Abstract
Inherited retinal diseases (IRDs) represent a collection of phenotypically and genetically diverse conditions. IRDs phenotype(s) can be isolated to the eye or can involve multiple tissues. These conditions are associated with diverse forms of inheritance, and variants within the same gene often can be associated with multiple distinct phenotypes. Such aspects of the IRDs highlight the difficulty met when establishing a genetic diagnosis in patients. Here we provide an overview of cutting-edge next-generation sequencing techniques and strategies currently in use to maximise the effectivity of IRD gene screening. These techniques have helped researchers globally to find elusive causes of IRDs, including copy number variants, structural variants, new IRD genes and deep intronic variants, among others. Resolving a genetic diagnosis with thorough testing enables a more accurate diagnosis and more informed prognosis and should also provide information on inheritance patterns which may be of particular interest to patients of a child-bearing age. Given that IRDs are heritable conditions, genetic counselling may be offered to help inform family planning, carrier testing and prenatal screening. Additionally, a verified genetic diagnosis may enable access to appropriate clinical trials or approved medications that may be available for the condition.
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Quinodoz M, Peter VG, Bedoni N, Royer Bertrand B, Cisarova K, Salmaninejad A, Sepahi N, Rodrigues R, Piran M, Mojarrad M, Pasdar A, Ghanbari Asad A, Sousa AB, Coutinho Santos L, Superti-Furga A, Rivolta C. AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data. Nat Commun 2021; 12:518. [PMID: 33483490 PMCID: PMC7822856 DOI: 10.1038/s41467-020-20584-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022] Open
Abstract
Homozygosity mapping is a powerful method for identifying mutations in patients with recessive conditions, especially in consanguineous families or isolated populations. Historically, it has been used in conjunction with genotypes from highly polymorphic markers, such as DNA microsatellites or common SNPs. Traditional software performs rather poorly with data from Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS), which are now extensively used in medical genetics. We develop AutoMap, a tool that is both web-based or downloadable, to allow performing homozygosity mapping directly on VCF (Variant Call Format) calls from WES or WGS projects. Following a training step on WES data from 26 consanguineous families and a validation procedure on a matched cohort, our method shows higher overall performances when compared with eight existing tools. Most importantly, when tested on real cases with negative molecular diagnosis from an internal set, AutoMap detects three gene-disease and multiple variant-disease associations that were previously unrecognized, projecting clear benefits for both molecular diagnosis and research activities in medical genetics. Homozygosity mapping is a useful tool for identifying candidate mutations in recessive conditions, however application to next generation sequencing data has been sub-optimal. Here, the authors present AutoMap, which efficiently identifies runs of homozygosity in whole exome/genome sequencing data.
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Affiliation(s)
- Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.,Institute of Experimental Pathology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Nicola Bedoni
- Service of Medical Genetics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Béryl Royer Bertrand
- Service of Medical Genetics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Katarina Cisarova
- Service of Medical Genetics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Arash Salmaninejad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Neda Sepahi
- Noncommunicable Diseases Research Center, Fasa University of Sciences, Fasa, Iran
| | - Raquel Rodrigues
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon Academic Medical Center (CAML), Lisbon, Portugal
| | - Mehran Piran
- Noncommunicable Diseases Research Center, Fasa University of Sciences, Fasa, Iran.,Bioinformatics and Computational Biology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Majid Mojarrad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Pasdar
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Division of Applied Medicine, Medical School, University of Aberdeen, Aberdeen, UK
| | - Ali Ghanbari Asad
- Noncommunicable Diseases Research Center, Fasa University of Sciences, Fasa, Iran
| | - Ana Berta Sousa
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon Academic Medical Center (CAML), Lisbon, Portugal.,Medical Faculty, Lisbon University, Lisbon, Portugal
| | | | - Andrea Superti-Furga
- Service of Medical Genetics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland. .,Department of Ophthalmology, University of Basel, Basel, Switzerland. .,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
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9
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Whole exome sequencing and homozygosity mapping reveals genetic defects in consanguineous Iranian families with inherited retinal dystrophies. Sci Rep 2020; 10:19413. [PMID: 33173045 PMCID: PMC7655865 DOI: 10.1038/s41598-020-75841-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/08/2020] [Indexed: 12/17/2022] Open
Abstract
Inherited retinal dystrophies (IRDs), displaying pronounced genetic and clinical heterogeneity, comprise of a broad range of diseases characterized by progressive retinal cell death and gradual loss of vision. By the combined use of whole exome sequencing (WES), SNP-array and WES-based homozygosity mapping, as well as directed DNA sequencing (Sanger), we have identified nine pathogenic variants in six genes (ABCA4, RPE65, MERTK, USH2A, SPATA7, TULP1) in 10 consanguineous Iranian families. Six of the nine identified variants were novel, including a putative founder mutation in ABCA4 (c.3260A>G, p.Glu1087Gly), detected in two families from Northeastern Iran. Our findings provide additional information to the molecular pathology of IRDs in Iran, hopefully contributing to better genetic counselling and patient management in the respective families from this country.
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10
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Ellingford JM, Hufnagel RB, Arno G. Phenotype and Genotype Correlations in Inherited Retinal Diseases: Population-Guided Variant Interpretation, Variable Expressivity and Incomplete Penetrance. Genes (Basel) 2020; 11:genes11111274. [PMID: 33137882 PMCID: PMC7692259 DOI: 10.3390/genes11111274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 12/15/2022] Open
Affiliation(s)
- Jamie M. Ellingford
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WL, UK
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
- Correspondence: (J.M.E.); (R.B.H.); (G.A.)
| | - Robert B. Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD 20016, USA
- Correspondence: (J.M.E.); (R.B.H.); (G.A.)
| | - Gavin Arno
- University College London Institute of Ophthalmology, London EC1V 9EL, UK
- Moorfields Eye Hospital, London EC1V 2PD, UK
- Correspondence: (J.M.E.); (R.B.H.); (G.A.)
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