1
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The Power of Clinical Diagnosis for Deciphering Complex Genetic Mechanisms in Rare Diseases. Genes (Basel) 2023; 14:genes14010196. [PMID: 36672937 PMCID: PMC9858967 DOI: 10.3390/genes14010196] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Complex genetic disease mechanisms, such as structural or non-coding variants, currently pose a substantial difficulty in frontline diagnostic tests. They thus may account for most unsolved rare disease patients regardless of the clinical phenotype. However, the clinical diagnosis can narrow the genetic focus to just a couple of genes for patients with well-established syndromes defined by prominent physical and/or unique biochemical phenotypes, allowing deeper analyses to consider complex genetic origin. Then, clinical-diagnosis-driven genome sequencing strategies may expedite the development of testing and analytical methods to account for complex disease mechanisms as well as to advance functional assays for the confirmation of complex variants, clinical management, and the development of new therapies.
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2
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Delvallée C, Dollfus H. Retinal Degeneration Animal Models in Bardet-Biedl Syndrome and Related Ciliopathies. Cold Spring Harb Perspect Med 2023; 13:13/1/a041303. [PMID: 36596648 PMCID: PMC9808547 DOI: 10.1101/cshperspect.a041303] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Retinal degeneration due to photoreceptor ciliary-related proteins dysfunction accounts for more than 25% of all inherited retinal dystrophies. The cilium, being an evolutionarily conserved and ubiquitous organelle implied in many cellular functions, can be investigated by way of many models from invertebrate models to nonhuman primates, all these models have massively contributed to the pathogenesis understanding of human ciliopathies. Taking the Bardet-Biedl syndrome (BBS) as an emblematic example as well as other related syndromic ciliopathies, the contribution of a wide range of models has enabled to characterize the role of the BBS proteins in the archetypical cilium but also at the level of the connecting cilium of the photoreceptors. There are more than 24 BBS genes encoding for proteins that form different complexes such as the BBSome and the chaperone proteins complex. But how they lead to retinal degeneration remains a matter of debate with the possible accumulation of proteins in the inner segment and/or accumulation of unwanted proteins in the outer segment that cannot return in the inner segment machinery. Many BBS proteins (but not the chaperonins for instance) can be modeled in primitive organisms such as Paramecium, Chlamydomonas reinardtii, Trypanosoma brucei, and Caenorhabditis elegans These models have enabled clarifying the role of a subset of BBS proteins in the primary cilium as well as their relations with other modules such as the intraflagellar transport (IFT) module, the nephronophthisis (NPHP) module, or the Meckel-Gruber syndrome (MKS)/Joubert syndrome (JBTS) module mostly involved with the transition zone of the primary cilia. Assessing the role of the primary cilia structure of the connecting cilium of the photoreceptor cells has been very much studied by way of zebrafish modeling (Danio rerio) as well as by a plethora of mouse models. More recently, large animal models have been described for three BBS genes and one nonhuman primate model in rhesus macaque for BBS7 In completion to animal models, human cell models can now be used notably thanks to gene editing and the use of induced pluripotent stem cells (iPSCs). All these models are not only important for pathogenesis understanding but also very useful for studying therapeutic avenues, their pros and cons, especially for gene replacement therapy as well as pharmacological triggers.
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Affiliation(s)
- Clarisse Delvallée
- Laboratoire de Génétique Médicale UMRS1112, Centre de Recherche Biomédicale de Strasbourg, CRBS, Institut de Génétique Médicale d'Alsace, IGMA, Strasbourg 67000, France
| | - Hélène Dollfus
- Laboratoire de Génétique Médicale UMRS1112, Centre de Recherche Biomédicale de Strasbourg, CRBS, Institut de Génétique Médicale d'Alsace, IGMA, Strasbourg 67000, France
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3
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Vezain M, Thauvin-Robinet C, Vial Y, Coutant S, Drunat S, Urtizberea JA, Rolland A, Jacquin-Piques A, Fehrenbach S, Nicolas G, Lecoquierre F, Saugier-Veber P. Retrotransposon insertion as a novel mutational cause of spinal muscular atrophy. Hum Genet 2023; 142:125-138. [PMID: 36138164 DOI: 10.1007/s00439-022-02473-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/15/2022] [Indexed: 01/18/2023]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder resulting from biallelic alterations of the SMN1 gene: deletion, gene conversion or, in rare cases, intragenic variants. The disease severity is mainly influenced by the copy number of SMN2, a nearly identical gene, which produces only low amounts of full-length (FL) mRNA. Here we describe the first example of retrotransposon insertion as a pathogenic SMN1 mutational event. The 50-year-old patient is clinically affected by SMA type III with a diagnostic odyssey spanning nearly 30 years. Despite a mild disease course, he carries a single SMN2 copy. Using Exome Sequencing and Sanger sequencing, we characterized a SINE-VNTR-Alu (SVA) type F retrotransposon inserted in SMN1 intron 7. Using RT-PCR and RNASeq experiments on lymphoblastoid cell lines, we documented the dramatic decrease of FL transcript production in the patient compared to subjects with the same SMN1 and SMN2 copy number, thus validating the pathogenicity of this SVA insertion. We described the mutant FL-SMN1-SVA transcript characterized by exon extension and showed that it is subject to degradation by nonsense-mediated mRNA decay. The stability of the SMN-SVA protein may explain the mild course of the disease. This observation exemplifies the role of retrotransposons in human genetic disorders.
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Affiliation(s)
- Myriam Vezain
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Christel Thauvin-Robinet
- INSERM UMR1231 GAD-Génétique des Anomalies du Développement, Bourgogne Franche-Comté University, F-21000 , Dijon, France.,Genetics Center, Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Dijon-Burgundy University Hospital, F-21000, Dijon, France
| | - Yoann Vial
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France.,Genetics Department, AP-HP, Robert-Debré University Hospital, 48 boulevard Sérurier, 75019 , Paris, France
| | - Sophie Coutant
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Séverine Drunat
- INSERM UMR 1141, PROTECT, Paris University, F-75019, Paris, France.,Genetics Department, AP-HP, Robert-Debré University Hospital, F-75019, Paris, France
| | - Jon Andoni Urtizberea
- Myology Institute, AP-HP Pitié-Salpêtrière University Hospital, F-75013, Paris, France
| | - Anne Rolland
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Pediatrics Department, Valence Hospital, 179 boulevard du Maréchal Juin, 26000, Valence, France
| | - Agnès Jacquin-Piques
- Department of Neurology, Clinical Neurophysiology, Competence Center of Neuromuscular Diseases, Dijon-Burgundy University Hospital, F-21000, Dijon, France
| | - Séverine Fehrenbach
- Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Gaël Nicolas
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - François Lecoquierre
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France.,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- INSERM UMR1245, UNIROUEN, Normandie Univ, F-76000, Rouen, France. .,Department of Genetics, FHU G4 Génomique, Rouen University Hospital, F-76000, Rouen, France. .,Laboratoire de Génétique Moléculaire, UFR-Santé, 22 boulevard Gambetta, 76183, Rouen, France.
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4
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Kõks S, Pfaff AL, Singleton LM, Bubb VJ, Quinn JP. Non-reference genome transposable elements (TEs) have a significant impact on the progression of the Parkinson's disease. Exp Biol Med (Maywood) 2022; 247:1680-1690. [PMID: 36000172 PMCID: PMC9597212 DOI: 10.1177/15353702221117147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The pathophysiology of Parkinson's disease (PD) is a complex process of the interaction between genetic and environmental factors. Studies on the genetic component of PD have predominantly focused on single nucleotide polymorphisms (SNPs) using a cross-sectional case-control design in large genome-wide association studies. This approach while giving insight into a significant portion of the genetics of PD does not fully account for all the genetic components resulting in missing heritability. In this study, we approached this problem by focusing on the non-reference genome transposable elements (TEs) and their impact on the progression of PD using a longitudinal study design within the Parkinson's progression markers initiative (PPMI) cohort. We analyzed 2886 Alu repeats, 360 LINE1 and 128 SINE-VNTR-Alus (SVAs) that were called from the whole-genome sequence data which are not within the reference genome. The presence or absence of these non-reference TE variants is known as a retrotransposon insertion polymorphism, and measuring this polymorphism describes the impact of TEs on the traits. The variations for the presence or absence of the non-reference TE elements were modeled to align with the changes in the 114 outcome measures during the five-year follow-up period of the PPMI cohort. Linear mixed-effects models were used, and many TEs were found to have a highly significant effect on the longitudinal changes in the clinically important PD outcomes such as UPDRS subscale II, UPDRS total scores, and modified Schwab and England ADL scale. In addition, the progression of several imaging and functional measures, including the Caudate/Putamen ratio and levodopa equivalent daily dose (LEDD) were also significantly affected by the TEs. In conclusion, this study identified the overwhelming effect of the non-reference TEs on the progression of PD and is a good example of the impact the variations in the "junk DNA" have on complex diseases.
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Affiliation(s)
- Sulev Kõks
- Perron Institute for Neurological and
Translational Science, Perth, WA 6009, Australia,Centre for Molecular Medicine and
Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia,Sulev Kõks.
| | - Abigail L Pfaff
- Perron Institute for Neurological and
Translational Science, Perth, WA 6009, Australia,Centre for Molecular Medicine and
Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Lewis M Singleton
- Perron Institute for Neurological and
Translational Science, Perth, WA 6009, Australia
| | - Vivien J Bubb
- Department of Pharmacology and
Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of
Liverpool, Liverpool L69 3BX, UK
| | - John P Quinn
- Department of Pharmacology and
Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of
Liverpool, Liverpool L69 3BX, UK
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5
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Dvaladze A, Tavares E, Di Scipio M, Nimmo G, Grudzinska-Pechhacker MK, Paton T, Tumber A, Li S, Eileen C, Ertl-Wagner B, Mamak E, Hoffmann G, Marshall CR, Haas D, Mayatepek E, Schulze A, Heon E, Vincent A. Deep Intronic Variant in MVK as a Cause for Mevalonic Aciduria Initially Presenting as Non-syndromic Retinitis Pigmentosa. Clin Genet 2022; 102:524-529. [PMID: 35916082 DOI: 10.1111/cge.14207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 07/25/2022] [Accepted: 07/27/2022] [Indexed: 11/29/2022]
Abstract
Non-syndromic retinitis pigmentosa (NSRP) is a clinically and genetically heterogeneous group of disorders characterized by progressive degeneration of the rod and cone photoreceptors, often leading to blindness. The evolving association of syndromic genes to cause NSRP and the increasing role of intronic variants in explaining missing heritability in genetic disorders present challenges in establishing conclusive clinical and genetic diagnoses. This study sought to identify and validate the causative genetic variant(s) in a 13-year-old male initially diagnosed with NSRP. Genome sequencing identified a pathogenic missense variant in MVK [NM_000431.3:c.803T>C (p. Ile268Thr)], in trans with a novel intronic variant predicted to create a new donor splice site (c.768+71C>A). Proband cDNA analysis confirmed the inclusion of the first 68 base pairs of intron 8 that resulted in a frameshift in MVK (r.768_769ins[768+1_768+68]) and significantly reduced the expression of reference transcript (17.6%). Patient re-phenotyping revealed ataxia, cerebellar atrophy, elevated urinary mevalonate and LTE4 , in keeping with mild mevalonic aciduria and associated syndromic retinitis pigmentosa. Leakage of reference transcript likely explains the milder phenotype observed. This is the first association of a deep intronic splice variant to cause MVK-related disorder. This report highlights the importance of variant validation and patient re-phenotyping in establishing accurate diagnosis in the era of genome sequencing.
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Affiliation(s)
- Anna Dvaladze
- Genetics and Genome Biology, The Hospital for Sick Children (HSC), Toronto, Canada
| | - Erika Tavares
- Genetics and Genome Biology, The Hospital for Sick Children (HSC), Toronto, Canada
| | - Matteo Di Scipio
- Genetics and Genome Biology, The Hospital for Sick Children (HSC), Toronto, Canada
| | - Graeme Nimmo
- Clinical and Metabolic Genetics, HSC, Canada.,Fred A Litwin Family Centre for Genetic Medicine, The University Health Network, Toronto, Canada
| | - Monika K Grudzinska-Pechhacker
- Genetics and Genome Biology, The Hospital for Sick Children (HSC), Toronto, Canada.,Department of Ophthalmology and Vision Sciences, HSC and University of Toronto, Canada
| | - Tara Paton
- The Centre for Applied Genomics, HSC, Canada
| | - Anupreet Tumber
- Department of Ophthalmology and Vision Sciences, HSC and University of Toronto, Canada
| | - Shuning Li
- Genetics and Genome Biology, The Hospital for Sick Children (HSC), Toronto, Canada
| | - Christabel Eileen
- Genetics and Genome Biology, The Hospital for Sick Children (HSC), Toronto, Canada
| | - Birgit Ertl-Wagner
- Division of Neuroradiology, HSC, Canada.,Department of Medical Imaging, University of Toronto, Canada
| | - Eva Mamak
- Department of Psychology, HSC, Canada
| | - Georg Hoffmann
- Neuropaediatrics and Paediatric Metabolic Medicine, University Hospital Heidelberg, Germany
| | | | - Dorothea Haas
- Neuropaediatrics and Paediatric Metabolic Medicine, University Hospital Heidelberg, Germany
| | - Ertan Mayatepek
- Department of General Paediatrics, Neonatology and Paediatric Cardiology, University Children's Hospital, Heinrich Heine University, Dusseldorf, Germany
| | - Andreas Schulze
- Clinical and Metabolic Genetics, HSC, Canada.,Department of Paediatrics, University of Toronto, Canada.,Department of Biochemistry, University of Toronto, Canada
| | - Elise Heon
- Genetics and Genome Biology, The Hospital for Sick Children (HSC), Toronto, Canada.,Department of Ophthalmology and Vision Sciences, HSC and University of Toronto, Canada
| | - Ajoy Vincent
- Genetics and Genome Biology, The Hospital for Sick Children (HSC), Toronto, Canada.,Department of Ophthalmology and Vision Sciences, HSC and University of Toronto, Canada
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6
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Pfaff AL, Singleton LM, Kõks S. Mechanisms of disease-associated SINE-VNTR-Alus. Exp Biol Med (Maywood) 2022; 247:756-764. [PMID: 35387528 DOI: 10.1177/15353702221082612] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
SINE-VNTR-Alus (SVAs) are the youngest retrotransposon family in the human genome. Their ongoing mobilization has generated genetic variation within the human population. At least 24 insertions to date, detailed in this review, have been associated with disease. The predominant mechanisms through which this occurs are alterations to normal splicing patterns, exonic insertions causing loss-of-function mutations, and large genomic deletions. Dissecting the functional impact of these SVAs and the mechanism through which they cause disease provides insight into the consequences of their presence in the genome and how these elements could influence phenotypes. Many of these disease-associated SVAs have been difficult to characterize and would not have been identified through routine analyses. However, the number identified has increased in recent years as DNA and RNA sequencing data became more widely available. Therefore, as the search for complex structural variation in disease continues, it is likely to yield further disease-causing SVA insertions.
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Affiliation(s)
- Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Lewis M Singleton
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
| | - Sulev Kõks
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.,Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
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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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8
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Bergant G, Maver A, Peterlin B. Whole-Genome Sequencing in Diagnostics of Selected Slovenian Undiagnosed Patients with Rare Disorders. Life (Basel) 2021; 11:life11030205. [PMID: 33807868 PMCID: PMC8001615 DOI: 10.3390/life11030205] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 02/24/2021] [Accepted: 03/01/2021] [Indexed: 11/16/2022] Open
Abstract
Several patients with rare genetic disorders remain undiagnosed following comprehensive diagnostic testing using whole-exome sequencing (WES). In these patients, pathogenic genetic variants may reside in intronic or regulatory regions or they may emerge through mutational mechanisms not detected by WES. For this reason, we implemented whole-genome sequencing (WGS) in routine clinical diagnostics of patients with undiagnosed genetic disorders and report on the outcome in 30 patients. Criteria for consideration included (1) negative WES, (2) a high likelihood of a genetic cause for the disorders, (3) positive family history, (4) detection of large blocks of homozygosity or (5) detection of a single pathogenic variant in a gene associated with recessive conditions. We successfully discovered a causative genetic variant in 6 cases, a retrotranspositional event in the APC gene, non-coding variants in the intronic region of the OTC gene and the promotor region of the UFM1 gene, repeat expansion in the RFC1 gene and a single exon duplication in the CNGB3 gene. We also discovered one coding variant, an indel, which was missed by variant caller during WES data analysis. Our study demonstrates the impact of WGS in the group of patients with undiagnosed genetic diseases after WES in the clinical setting and the diversity of mutational mechanisms discovered, which would remain undetected using other methods.
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9
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Di Scipio M, Tavares E, Deshmukh S, Audo I, Green-Sanderson K, Zubak Y, Zine-Eddine F, Pearson A, Vig A, Tang CY, Mollica A, Karas J, Tumber A, Yu CW, Billingsley G, Wilson MD, Zeitz C, Héon E, Vincent A. Phenotype Driven Analysis of Whole Genome Sequencing Identifies Deep Intronic Variants that Cause Retinal Dystrophies by Aberrant Exonization. Invest Ophthalmol Vis Sci 2021; 61:36. [PMID: 32881472 PMCID: PMC7443117 DOI: 10.1167/iovs.61.10.36] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Purpose To demonstrate the effectiveness of combining retinal phenotyping and focused variant filtering from genome sequencing (GS) in identifying deep intronic disease causing variants in inherited retinal dystrophies. Methods Affected members from three pedigrees with classical enhanced S-cone syndrome (ESCS; Pedigree 1), congenital stationary night blindness (CSNB; Pedigree 2), and achromatopsia (ACHM; Pedigree 3), respectively, underwent detailed ophthalmologic evaluation, optical coherence tomography, and electroretinography. The probands underwent panel-based genetic testing followed by GS analysis. Minigene constructs (NR2E3, GPR179 and CNGB3) and patient-derived cDNA experiments (NR2E3 and GPR179) were performed to assess the functional effect of the deep intronic variants. Results The electrophysiological findings confirmed the clinical diagnosis of ESCS, CSNB, and ACHM in the respective pedigrees. Panel-based testing revealed heterozygous pathogenic variants in NR2E3 (NM_014249.3; c.119-2A>C; Pedigree 1) and CNGB3 (NM_019098.4; c.1148delC/p.Thr383Ilefs*13; Pedigree 3). The GS revealed heterozygous deep intronic variants in Pedigrees 1 (NR2E3; c.1100+1124G>A) and 3 (CNGB3; c.852+4751A>T), and a homozygous GPR179 variant in Pedigree 2 (NM_001004334.3; c.903+343G>A). The identified variants segregated with the phenotype in all pedigrees. All deep intronic variants were predicted to generate a splice acceptor gain causing aberrant exonization in NR2E3 [89 base pairs (bp)], GPR179 (197 bp), and CNGB3 (73 bp); splicing defects were validated through patient-derived cDNA experiments and/or minigene constructs and rescued by antisense oligonucleotide treatment. Conclusions Deep intronic mutations contribute to missing heritability in retinal dystrophies. Combining results from phenotype-directed gene panel testing, GS, and in silico splice prediction tools can help identify these difficult-to-detect pathogenic deep intronic variants.
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Affiliation(s)
- Matteo Di Scipio
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Erika Tavares
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Shriya Deshmukh
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.,CHNO des Quinze-Vingts, INSERM-DGOS CIC1423, Paris, France.,University College London Institute of Ophthalmology, London, United Kingdom
| | - Kit Green-Sanderson
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Yuliya Zubak
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Fayçal Zine-Eddine
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Alexander Pearson
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Anjali Vig
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Chen Yu Tang
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Antonio Mollica
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Jonathan Karas
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Anupreet Tumber
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Canada
| | - Caberry W Yu
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Gail Billingsley
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Michael D Wilson
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Elise Héon
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Canada.,Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada
| | - Ajoy Vincent
- Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Canada.,Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, Canada
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10
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Delvallée C, Nicaise S, Antin M, Leuvrey AS, Nourisson E, Leitch CC, Kellaris G, Stoetzel C, Geoffroy V, Scheidecker S, Keren B, Depienne C, Klar J, Dahl N, Deleuze JF, Génin E, Redon R, Demurger F, Devriendt K, Mathieu-Dramard M, Poitou-Bernert C, Odent S, Katsanis N, Mandel JL, Davis EE, Dollfus H, Muller J. A BBS1 SVA F retrotransposon insertion is a frequent cause of Bardet-Biedl syndrome. Clin Genet 2020; 99:318-324. [PMID: 33169370 DOI: 10.1111/cge.13878] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/04/2020] [Accepted: 11/06/2020] [Indexed: 12/11/2022]
Abstract
Bardet-Biedl syndrome (BBS) is a ciliopathy characterized by retinitis pigmentosa, obesity, polydactyly, cognitive impairment and renal failure. Pathogenic variants in 24 genes account for the molecular basis of >80% of cases. Toward saturated discovery of the mutational basis of the disorder, we carefully explored our cohorts and identified a hominid-specific SINE-R/VNTR/Alu type F (SVA-F) insertion in exon 13 of BBS1 in eight families. In six families, the repeat insertion was found in trans with c.1169 T > G, p.Met390Arg and in two families the insertion was found in addition to other recessive BBS loci. Whole genome sequencing, de novo assembly and SNP array analysis were performed to characterize the genomic event. This insertion is extremely rare in the general population (found in 8 alleles of 8 BBS cases but not in >10 800 control individuals from gnomAD-SV) and due to a founder effect. Its 2435 bp sequence contains hallmarks of LINE1 mediated retrotransposition. Functional studies with patient-derived cell lines confirmed that the BBS1 SVA-F is deleterious as evidenced by a significant depletion of both mRNA and protein levels. Such findings highlight the importance of dedicated bioinformatics pipelines to identify all types of variation.
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Affiliation(s)
- Clarisse Delvallée
- Laboratoire de Génétique Médicale, Institut de génétique médicale d'Alsace IGMA, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg UMRS_1112, Strasbourg, France
| | - Samuel Nicaise
- Laboratoire de Génétique Médicale, Institut de génétique médicale d'Alsace IGMA, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg UMRS_1112, Strasbourg, France
| | - Manuela Antin
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Anne-Sophie Leuvrey
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Elsa Nourisson
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Carmen C Leitch
- Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Georgios Kellaris
- Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Corinne Stoetzel
- Laboratoire de Génétique Médicale, Institut de génétique médicale d'Alsace IGMA, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg UMRS_1112, Strasbourg, France
| | - Véronique Geoffroy
- Laboratoire de Génétique Médicale, Institut de génétique médicale d'Alsace IGMA, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg UMRS_1112, Strasbourg, France
| | - Sophie Scheidecker
- Laboratoire de Génétique Médicale, Institut de génétique médicale d'Alsace IGMA, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg UMRS_1112, Strasbourg, France.,Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Boris Keren
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, Paris, France.,AP-HP, Hôpital de la Pitié-Salpêtrière, Département de Génétique, Paris, France
| | - Christel Depienne
- Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, Paris, France.,Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Joakim Klar
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de biologie François Jacob, Evry, France
| | | | - Richard Redon
- Université de Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Florence Demurger
- Service de Génétique Médicale, Centre Hospitalier Bretagne Atlantique, Vannes, France
| | - Koenraad Devriendt
- Center for Human Genetics, University Hospital Leuven and KU Leuven, Leuven, Belgium
| | | | - Christine Poitou-Bernert
- Assistance Publique Hôpitaux de Paris, Nutrition Department Pitié-Salpêtrière Hospital; Sorbonne Université, INSERM, NutriOmics Research Unit, Paris, France
| | - Sylvie Odent
- Centre de Référence Maladies Rares CLAD-Ouest, Service de Génétique Clinique, CHU Rennes, Rennes, France.,CNRS, IGDR (Institut de Génétique et Développement de Rennes) UMR 6290, Université de Rennes, Rennes, France
| | - Nicholas Katsanis
- Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA.,Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Jean-Louis Mandel
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U964, Université de Strasbourg, Dept Transl Med and Neurogenetics Illkirch, France
| | - Erica E Davis
- Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA.,Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Hélène Dollfus
- Laboratoire de Génétique Médicale, Institut de génétique médicale d'Alsace IGMA, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg UMRS_1112, Strasbourg, France.,Service de Génétique Médicale, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Filière SENSGENE, Centre de Référence pour les affections rares en génétique ophtalmologique, CARGO, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Jean Muller
- Laboratoire de Génétique Médicale, Institut de génétique médicale d'Alsace IGMA, INSERM U1112, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg UMRS_1112, Strasbourg, France.,Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
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11
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Damert A. LINE-1 ORF1p does not determine substrate preference for human/orangutan SVA and gibbon LAVA. Mob DNA 2020; 11:27. [PMID: 32676128 PMCID: PMC7353768 DOI: 10.1186/s13100-020-00222-y] [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: 03/02/2020] [Accepted: 07/06/2020] [Indexed: 12/28/2022] Open
Abstract
Background Non-autonomous VNTR (Variable Number of Tandem Repeats) composite retrotransposons – SVA (SINE-R-VNTR-Alu) and LAVA (L1-Alu-VNTR-Alu) – are specific to hominoid primates. SVA expanded in great apes, LAVA in gibbon. Both SVA and LAVA have been shown to be mobilized by the autonomous LINE-1 (L1)-encoded protein machinery in a cell-based assay in trans. The efficiency of human SVA retrotransposition in vitro has, however, been considerably lower than would be expected based on recent pedigree-based in vivo estimates. The VNTR composite elements across hominoids – gibbon LAVA, orangutan SVA_A descendants and hominine SVA_D descendants – display characteristic structures of the 5′ Alu-like domain and the VNTR. Different partner L1 subfamilies are currently active in each of the lineages. The possibility that the lineage-specific types of VNTR composites evolved in response to evolutionary changes in their autonomous partners, particularly in the nucleic acid binding L1 ORF1-encoded protein, has not been addressed. Results Here I report the identification and functional characterization of a highly active human SVA element using an improved mneo retrotransposition reporter cassette. The modified cassette (mneoM) minimizes splicing between the VNTR of human SVAs and the neomycin phosphotransferase stop codon. SVA deletion analysis provides evidence that key elements determining its mobilization efficiency reside in the VNTR and 5′ hexameric repeats. Simultaneous removal of the 5′ hexameric repeats and part of the VNTR has an additive negative effect on mobilization rates. Taking advantage of the modified reporter cassette that facilitates robust cross-species comparison of SVA/LAVA retrotransposition, I show that the ORF1-encoded proteins of the L1 subfamilies currently active in gibbon, orangutan and human do not display substrate preference for gibbon LAVA versus orangutan SVA versus human SVA. Finally, I demonstrate that an orangutan-derived ORF1p supports only limited retrotransposition of SVA/LAVA in trans, despite being fully functional in L1 mobilization in cis. Conclusions Overall, the analysis confirms SVA as a highly active human retrotransposon and preferred substrate of the L1-encoded protein machinery. Based on the results obtained in human cells coevolution of L1 ORF1p and VNTR composites does not appear very likely. The changes in orangutan L1 ORF1p that markedly reduce its mobilization capacity in trans might explain the different SVA insertion rates in the orangutan and hominine lineages, respectively.
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Affiliation(s)
- Annette Damert
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
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12
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Jones KD, Radziwon A, Birch DG, MacDonald IM. A novel SVA retrotransposon insertion in the CHM gene results in loss of REP-1 causing choroideremia. Ophthalmic Genet 2020; 41:341-344. [PMID: 32441177 DOI: 10.1080/13816810.2020.1768557] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
BACKGROUND Choroideremia is an X-linked retinal disease characterized by progressive atrophy of the choroid and retinal pigment epithelium caused by mutations in the CHM gene. SVA (SINE-R/VNTR/Alu) elements are a type of non-autonomous retrotransposon that occasionally self-replicate, reinsert randomly into a gene, and cause disease. Intragenic SVA insertions have been reported as the mechanism underlying a number of diseases including a syndromic form of retinal dystrophy, but have never been found in CHM. MATERIALS AND METHODS Here we identified and characterized a novel hemizygous SVA insertion, c.97_98inSVA (p.Arg33insSVA), in exon 2 of CHM in a male choroideremia patient. The SVA insertion's impact was evaluated by establishing a patient-derived lymphoblastoid cell line as a source of RNA for mRNA analysis of the CHM transcript, and protein for immunoblot analysis of Rab Escort Protein 1 (REP-1). RESULTS Immunoblot analysis revealed the absence of REP-1 protein, while a smaller than expected PCR product was amplified from cDNA. Sequencing of this PCR product showed skipping of exon 2, denoted r.50_116del. Ophthalmic examination including psychophysical tests, visual electrophysiology, and fundus imaging showed the patient's phenotype was consistent with severe early manifestations of choroideremia. CONCLUSIONS This case is the first report of a SVA insertion in the CHM gene causing choroideremia.
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Affiliation(s)
| | - Alina Radziwon
- Department of Ophthalmology and Visual Sciences, University of Alberta , Edmonton, Alberta, Canada
| | - David G Birch
- Retina Foundation of the S.W ., Dallas, TX, USA.,Ophthalmology, UTSW Medical Center , Dallas, TX, USA
| | - Ian M MacDonald
- Department of Ophthalmology and Visual Sciences, University of Alberta , Edmonton, Alberta, Canada
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13
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Copy-number variation contributes 9% of pathogenicity in the inherited retinal degenerations. Genet Med 2020; 22:1079-1087. [PMID: 32037395 PMCID: PMC7272325 DOI: 10.1038/s41436-020-0759-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/27/2020] [Indexed: 11/08/2022] Open
Abstract
PURPOSE Current sequencing strategies can genetically solve 55-60% of inherited retinal degeneration (IRD) cases, despite recent progress in sequencing. This can partially be attributed to elusive pathogenic variants (PVs) in known IRD genes, including copy-number variations (CNVs), which have been shown as major contributors to unsolved IRD cases. METHODS Five hundred IRD patients were analyzed with targeted next-generation sequencing (NGS). The NGS data were used to detect CNVs with ExomeDepth and gCNV and the results were compared with CNV detection with a single-nucleotide polymorphism (SNP) array. Likely causal CNV predictions were validated by quantitative polymerase chain reaction (qPCR). RESULTS Likely disease-causing single-nucleotide variants (SNVs) and small indels were found in 55.6% of subjects. PVs in USH2A (11.6%), RPGR (4%), and EYS (4%) were the most common. Likely causal CNVs were found in an additional 8.8% of patients. Of the three CNV detection methods, gCNV showed the highest accuracy. Approximately 30% of unsolved subjects had a single likely PV in a recessive IRD gene. CONCLUSION CNV detection using NGS-based algorithms is a reliable method that greatly increases the genetic diagnostic rate of IRDs. Experimentally validating CNVs helps estimate the rate at which IRDs might be solved by a CNV plus a more elusive variant.
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14
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Maroilley T, Tarailo-Graovac M. Uncovering Missing Heritability in Rare Diseases. Genes (Basel) 2019; 10:E275. [PMID: 30987386 PMCID: PMC6523881 DOI: 10.3390/genes10040275] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 12/14/2022] Open
Abstract
The problem of 'missing heritability' affects both common and rare diseases hindering: discovery, diagnosis, and patient care. The 'missing heritability' concept has been mainly associated with common and complex diseases where promising modern technological advances, like genome-wide association studies (GWAS), were unable to uncover the complete genetic mechanism of the disease/trait. Although rare diseases (RDs) have low prevalence individually, collectively they are common. Furthermore, multi-level genetic and phenotypic complexity when combined with the individual rarity of these conditions poses an important challenge in the quest to identify causative genetic changes in RD patients. In recent years, high throughput sequencing has accelerated discovery and diagnosis in RDs. However, despite the several-fold increase (from ~10% using traditional to ~40% using genome-wide genetic testing) in finding genetic causes of these diseases in RD patients, as is the case in common diseases-the majority of RDs are also facing the 'missing heritability' problem. This review outlines the key role of high throughput sequencing in uncovering genetics behind RDs, with a particular focus on genome sequencing. We review current advances and challenges of sequencing technologies, bioinformatics approaches, and resources.
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Affiliation(s)
- Tatiana Maroilley
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada.
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada.
| | - Maja Tarailo-Graovac
- Departments of Biochemistry, Molecular Biology and Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada.
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada.
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15
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Tavares E, Tang CY, Vig A, Li S, Billingsley G, Sung W, Vincent A, Thiruvahindrapuram B, Héon E. Retrotransposon insertion as a novel mutational event in Bardet-Biedl syndrome. Mol Genet Genomic Med 2018; 7:e00521. [PMID: 30484961 PMCID: PMC6393654 DOI: 10.1002/mgg3.521] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/23/2018] [Accepted: 10/26/2018] [Indexed: 01/12/2023] Open
Abstract
Background Bardet‐Biedl syndrome (BBS) is an autosomal recessive pleiotropic disorder of the primary cilia that leads to severe visual loss in the teenage years. Approximately 80% of BBS cases are explained by mutations in one of the 21 identified genes. Documented causative mutation types include missense, nonsense, copy number variation (CNV), frameshift deletions or insertions, and splicing variants. Methods Whole genome sequencing was performed on a patient affected with BBS for whom no mutations were identified using clinically approved genetic testing of the known genes. Analysis of the WGS was done using internal protocols and publicly available algorithms. The phenotype was defined by retrospective chart review. Results We document a female affected with BBS carrying the most common BBS1 mutation (BBS1: Met390Arg) on the maternal allele and an insertion of a ~1.7‐kb retrotransposon in exon 13 on the paternal allele. This retrotransposon insertion was not automatically annotated by the standard variant calling protocols used. This novel variant was identified by visual inspection of the alignment file followed by specific genome analysis with an available algorithm for transposable elements. Conclusion This report documents a novel mutation type associated with BBS and highlights the importance of systematically performing transposon detection analysis on WGS data of unsolved cases.
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Affiliation(s)
- Erika Tavares
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Chen Yu Tang
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anjali Vig
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Shuning Li
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gail Billingsley
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Wilson Sung
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ajoy Vincent
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.,Ophthalmology and Vision Sciences, Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Elise Héon
- Genetics and Genome Biology, Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.,Ophthalmology and Vision Sciences, Hospital for Sick Children, Toronto, Ontario, Canada
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