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Babu HWS, Elangovan A, Iyer M, Kirola L, Muthusamy S, Jeeth P, Muthukumar S, Vanlalpeka H, Gopalakrishnan AV, Kadhirvel S, Kumar NS, Vellingiri B. Association Study Between Kynurenine 3-Monooxygenase (KMO) Gene and Parkinson's Disease Patients. Mol Neurobiol 2024; 61:3867-3881. [PMID: 38040995 DOI: 10.1007/s12035-023-03815-9] [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: 09/26/2023] [Accepted: 11/18/2023] [Indexed: 12/03/2023]
Abstract
The influence of various risk factors such as aging, intricate cellular molecular processes, and lifestyle factors like smoking, alcohol consumption, caffeine intake, and occupational factors has received increased focus in relation to the risk and development of Parkinson's disease (PD). Limited research has been conducted on the assessment of lifestyle impact on kynurenine 3-monooxygenase (KMO) gene in PD. A total of 164 subjects, including 82 PD cases and 82 healthy individuals, were recruited based on specific inclusion and exclusion criteria. The severity of PD and clinical assessment were evaluated using the Unified Parkinson's Disease Rating Scale (UPDRS) and Hoehn and Yahr (HY) scaling. Sanger sequencing was performed to analyse the KMO gene in the recruited subjects, and case-control studies were conducted. The UPDRS assessment revealed significant impairments in smell, tremors, walking, and posture instability in the late-onset PD cohorts. The HY scaling indicated a higher proportion of late-onset cohorts in stage 2. Moreover, both alcoholic and non-alcoholic groups showed significantly increased levels of 3-HK in late-onset PD. Gene analysis identified missense variants at position g.241593373 T > A (rs752312199) and intronic variants at positions g.241592623A > G (rs640718), g.241592800C > A (rs990388262), g.241592802A > C (rs1350160268), g.241592808 T > C (rs1478255936), and g.241592812G > T (rs948928931). The alterations in the KMO gene were found to influence the levels of kynurenic acid (KYNA) and 3-hydroxykynurenine (3-HK). Genomic analysis revealed a high prevalence of missense mutations in the late-onset PD groups, leading to a decline in 3-HK levels in patients. This leads to the reduction of the progression of disease in late-onset groups which shows that this mutation may lead to the protective effect on the PD subjects. This study suggests the use of KYNA and 3-HK as potential biomarkers in analysing the progression of disease. This study is limited by its small sample size. To overcome this limitation, a larger study involving in greater number of participants is needed to thoroughly investigate the KMO gene and KP metabolites, to enhance our understanding of Parkinson's disease progression, and to enhance diagnostic capabilities.
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Affiliation(s)
- Harysh Winster Suresh Babu
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, 641 046, Tamil Nadu, India
- Stem Cell and Regenerative Medicine, Translational Research, Department of Zoology, School of Basic Sciences, Central University of Punjab, Bathinda, 151401, Punjab, India
| | - Ajay Elangovan
- Stem Cell and Regenerative Medicine, Translational Research, Department of Zoology, School of Basic Sciences, Central University of Punjab, Bathinda, 151401, Punjab, India
| | - Mahalaxmi Iyer
- Department of Microbiology, School of Basic Sciences, Central University of Punjab, Bathinda, 151401, Punjab, India
- Centre for Neuroscience, Department of Biotechnology, Karpagam Academy of Higher Education (Deemed to be University), Coimbatore, India
| | - Laxmi Kirola
- Amity Institute of Biotechnology, Amity University, Noida, 201301, India
- Department of Biotechnology, School of Health Sciences and Technology (SoHST), UPES University, Dehradun, 248007, Uttarakhand, India
| | - Sureshan Muthusamy
- School of Chemical & Biotechnology, SASTRA Deemed University, Thanjavur, 613401, India
| | - Priyanka Jeeth
- Structural and Computational Biology Laboratory, Department of Computational Sciences, Central University of Punjab, 151401, Bathinda, Punjab, India
| | - Sindduja Muthukumar
- Stem Cell and Regenerative Medicine, Translational Research, Department of Zoology, School of Basic Sciences, Central University of Punjab, Bathinda, 151401, Punjab, India
| | - Harvey Vanlalpeka
- Department of Obstetrics and Gynaecology, Zoram Medical College, Falkawn, 796005, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Tamil Nadu, Vellore, 632 014, India
| | - Saraboji Kadhirvel
- Structural and Computational Biology Laboratory, Department of Computational Sciences, Central University of Punjab, 151401, Bathinda, Punjab, India
| | | | - Balachandar Vellingiri
- Stem Cell and Regenerative Medicine, Translational Research, Department of Zoology, School of Basic Sciences, Central University of Punjab, Bathinda, 151401, Punjab, India.
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Zeitz C, Navarro J, Azizzadeh Pormehr L, Méjécase C, Neves LM, Letellier C, Condroyer C, Albadri S, Amprou A, Antonio A, Ben-Yacoub T, Wohlschlegel J, Andrieu C, Serafini M, Bianco L, Antropoli A, Nassisi M, El Shamieh S, Chantot-Bastaraud S, Mohand-Saïd S, Smirnov V, Sahel JA, Del Bene F, Audo I. Variants in UBAP1L lead to autosomal recessive rod-cone and cone-rod dystrophy. Genet Med 2024; 26:101081. [PMID: 38293907 DOI: 10.1016/j.gim.2024.101081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/01/2024] Open
Abstract
PURPOSE Progressive inherited retinal degenerations (IRDs) affecting rods and cones are clinically and genetically heterogeneous and can lead to blindness with limited therapeutic options. The major gene defects have been identified in subjects of European and Asian descent with only few reports of North African descent. METHODS Genome, targeted next-generation, and Sanger sequencing was applied to cohort of ∼4000 IRDs cases. Expression analyses were performed including Chip-seq database analyses, on human-derived retinal organoids (ROs), retinal pigment epithelium cells, and zebrafish. Variants' pathogenicity was accessed using 3D-modeling and/or ROs. RESULTS Here, we identified a novel gene defect with three distinct pathogenic variants in UBAP1L in 4 independent autosomal recessive IRD cases from Tunisia. UBAP1L is expressed in the retinal pigment epithelium and retina, specifically in rods and cones, in line with the phenotype. It encodes Ubiquitin-associated protein 1-like, containing a solenoid of overlapping ubiquitin-associated domain, predicted to interact with ubiquitin. In silico and in vitro studies, including 3D-modeling and ROs revealed that the solenoid of overlapping ubiquitin-associated domain is truncated and thus ubiquitin binding most likely abolished secondary to all variants identified herein. CONCLUSION Biallelic UBAP1L variants are a novel cause of IRDs, most likely enriched in the North African population.
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Affiliation(s)
- Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France.
| | - Julien Navarro
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Leila Azizzadeh Pormehr
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Mass. Eye and Ear, Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Harvard Medical School, Boston, MA
| | - Cécile Méjécase
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; UCL Institute of Ophthalmology, London, UK; The Francis Crick Institute, London, UK
| | - Luiza M Neves
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Instituto Nacional de Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Camille Letellier
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Shahad Albadri
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Andréa Amprou
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Aline Antonio
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Tasnim Ben-Yacoub
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Juliette Wohlschlegel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Department of Biological Structure, University of Washington, Seattle, WA
| | - Camille Andrieu
- Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Centre de Référence Maladies Rares REFERET and INSERM-DGOS CIC 1423, Paris, France
| | - Malo Serafini
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Lorenzo Bianco
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Department of Ophthalmology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessio Antropoli
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Department of Ophthalmology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marco Nassisi
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Said El Shamieh
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Molecular Testing Laboratory, Department of Medical Laboratory Technology, Faculty of Health Sciences, Beirut Arab University, Beirut, Lebanon
| | - Sandra Chantot-Bastaraud
- APHP, Hôpital Armand-Trousseau, Département de Génétique, UF de Génétique Chromosomique, Paris, France
| | - Saddek Mohand-Saïd
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Centre de Référence Maladies Rares REFERET and INSERM-DGOS CIC 1423, Paris, France
| | - Vasily Smirnov
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Exploration de la Vision et Neuro-Ophtalmologie, CHU de Lille, Lille, France
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Centre de Référence Maladies Rares REFERET and INSERM-DGOS CIC 1423, Paris, France; Department of Ophthalmology, The University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Filippo Del Bene
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France; Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, Centre de Référence Maladies Rares REFERET and INSERM-DGOS CIC 1423, Paris, France.
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De Angeli P, Flores-Tufiño A, Stingl K, Kühlewein L, Roschi E, Wissinger B, Kohl S. Splicing defects and CRISPR-Cas9 correction in isogenic homozygous photoreceptor precursors harboring clustered deep-intronic ABCA4 variants. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102113. [PMID: 38274366 PMCID: PMC10809099 DOI: 10.1016/j.omtn.2023.102113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024]
Abstract
Splicing defects from deep-intronic variants significantly contribute to the mutational spectrum in ABCA4-associated inherited retinal diseases, necessitating functional validation for their pathological classification. Typically, minigene assays in HEK293(T) can qualitatively assess splicing defects, yet they often fail to quantitatively reproduce the resulting mis-splicing patterns, leaving uncertainty on severity and pathogenicity. As a potential cellular model derived from patient cells, photoreceptor precursor cells (PPCs) play a pivotal role in assessing the severity of specific splicing mutations. Nevertheless, the accessibility of biosamples is commonly constrained, and their establishment is costly and laborious. In this study, we combined and investigated the use of a minigene assay and isogenic PPCs, as superior qualitative and more accessible cellular models for the assessment of splicing defects. Specifically, we focused on the clustered c.5196+1013A>G, c.5196+1056A>G, and c.5196+1216C>A deep-intronic variants in intron 36 of ABCA4, comparing their resulting (mis)splicing patterns in minigene-transfected cells and isogenic CRISPR-Cas9-knocked-in PPCs harboring these pathogenic variants in homozygous state. Moreover, we demonstrate the successful correction of these three splicing defects in homozygous mutant PPCs using a single pair of guide RNAs to target Cas9 cleavage, thereby identifying an efficient gene editing strategy for therapeutic applications.
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Affiliation(s)
- Pietro De Angeli
- Institute for Ophthalmic Research, Centre for Ophthalmology, University Clinics Tübingen, Elfriede-Aulhorn-Str. 7, 72076 Tübingen, Germany
| | - Arturo Flores-Tufiño
- Institute for Ophthalmic Research, Centre for Ophthalmology, University Clinics Tübingen, Elfriede-Aulhorn-Str. 7, 72076 Tübingen, Germany
| | - Katarina Stingl
- University Eye Hospital, Centre for Ophthalmology, University Clinics Tübingen, Elfriede-Aulhorn-Str. 7, 72076 Tübingen, Germany
| | - Laura Kühlewein
- University Eye Hospital, Centre for Ophthalmology, University Clinics Tübingen, Elfriede-Aulhorn-Str. 7, 72076 Tübingen, Germany
| | - Eleonora Roschi
- Institute for Ophthalmic Research, Centre for Ophthalmology, University Clinics Tübingen, Elfriede-Aulhorn-Str. 7, 72076 Tübingen, Germany
- Wellcome Sanger Institute, Hinxton CB10 1RQ, Saffron Walden, UK
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for Ophthalmology, University Clinics Tübingen, Elfriede-Aulhorn-Str. 7, 72076 Tübingen, Germany
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for Ophthalmology, University Clinics Tübingen, Elfriede-Aulhorn-Str. 7, 72076 Tübingen, Germany
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Liu X, Hu F, Zhang D, Li Z, He J, Zhang S, Wang Z, Zhao Y, Wu J, Liu C, Li C, Li X, Wu J. Whole genome sequencing enables new genetic diagnosis for inherited retinal diseases by identifying pathogenic variants. NPJ Genom Med 2024; 9:6. [PMID: 38245557 PMCID: PMC10799956 DOI: 10.1038/s41525-024-00391-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/19/2023] [Indexed: 01/22/2024] Open
Abstract
Inherited retinal diseases (IRDs) are a group of common primary retinal degenerative disorders. Conventional genetic testing strategies, such as panel-based sequencing and whole exome sequencing (WES), can only elucidate the genetic etiology in approximately 60% of IRD patients. Studies have suggested that unsolved IRD cases could be attributed to previously undetected structural variants (SVs) and intronic variants in IRD-related genes. The aim of our study was to obtain a definitive genetic diagnosis by employing whole genome sequencing (WGS) in IRD cases where the causative genes were inconclusive following an initial screening by panel sequencing. A total of 271 unresolved IRD patients and their available family members (n = 646) were screened using WGS to identify pathogenic SVs and intronic variants in 792 known ocular disease genes. Overall, 13% (34/271) of IRD patients received a confirmed genetic diagnosis, among which 7% were exclusively attributed to SVs, 4% to a combination of single nucleotide variants (SNVs) and SVs while another 2% were linked to intronic variants. 22 SVs, 3 deep-intronic variants, and 2 non-canonical splice-site variants across 14 IRD genes were identified in the entire cohort. Notably, all of these detected SVs and intronic variants were novel pathogenic variants. Among those, 74% (20/27) of variants were found in genes causally linked to Retinitis Pigmentosa (RP), with the gene EYS being the most frequently affected by SVs. The identification of SVs and intronic variants through WGS enhances the genetic diagnostic yield of IRDs and broadens the mutational spectrum of known IRD-associated genes.
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Affiliation(s)
- Xubing Liu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fangyuan Hu
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Daowei Zhang
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Zhe Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jianquan He
- Computer Center, Eye & ENT Hospital, Fudan University, Shanghai, China
| | - Shenghai Zhang
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Zhenguo Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yingke Zhao
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Jiawen Wu
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Chen Liu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chenchen Li
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Xin Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Jihong Wu
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China.
- NHC Key Laboratory of Myopia (Fudan University); Key Laboratory of Myopia, Chinese Academy of Medical Sciences, Shanghai, China.
- Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China.
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Tian L, Chen CJ, Song YN, Xu K, Li NE, Zhang XH, Xie Y, Jin ZB, Li Y. Comprehensive genetic analysis reveals the mutational landscape of ABCA4-associated retinal dystrophy in a Chinese cohort. Gene 2024; 891:147832. [PMID: 37774808 DOI: 10.1016/j.gene.2023.147832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 09/15/2023] [Accepted: 09/25/2023] [Indexed: 10/01/2023]
Abstract
PURPOSE To depict the variant profiles of the ABCA4 gene in a large Chinese cohort of patients with ABCA4-associated retinal dystrophy (ABCA4-RD). METHODS We recruited 290 unrelated Chinese patients with ABCA4-RD and did ABCA4 mutational screening by a combination of Sanger sequencing, targeted exome sequencing, entire ABCA4 locus sequencing, and whole genome sequencing (WGS). The pathogenicity of variants was assessed using in silico tools or in vitro splicing assays following the American College of Medical Genetics and Genomics guidelines. RESULTS Two hundred sixty-eight distinct pathogenic variants were identified, and 57 were novel. In 580 alleles, 22 noncoding region variants outside canonical splice sites and 4 structural variations were found in 44 alleles accounting for 7.6% of all alleles. Bioinformatics analysis showed the complex mechanism of aberrant splicing productsnatural splice site disruption, branch point destruction, and cryptic splice site activation. Correspondingly, minigene assays validated the various abnormal splicing products, including exon skipping, exon elongation, partial exon deletion, and pseudoexon insertion. WGS identified the first inversion variation in ABCA4. CONCLUSIONS This study systematically depicted the variant profiles of ABCA4 and revealed the missing alleles of patients with ABCA4-RD in a large Chinese cohort. Our findings demonstrated the complexity of molecular diagnosis of Mendelian diseases and the efficiency of WGS for detecting structural variants.
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Affiliation(s)
- Lu Tian
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China; Department of Ophthalmology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Chun-Jie Chen
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Yu-Ning Song
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Ke Xu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Ni-En Li
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Xiao-Hui Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Yue Xie
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Yang Li
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China.
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Lenassi E, Carvalho A, Thormann A, Abrahams L, Arno G, Fletcher T, Hardcastle C, Lopez J, Hunt SE, Short P, Sergouniotis PI, Michaelides M, Webster A, Cunningham F, Ramsden SC, Kasperaviciute D, Fitzpatrick DR, Black GC, Ellingford JM. EyeG2P: an automated variant filtering approach improves efficiency of diagnostic genomic testing for inherited ophthalmic disorders. J Med Genet 2023; 60:810-818. [PMID: 36669873 PMCID: PMC10423522 DOI: 10.1136/jmg-2022-108618] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 12/16/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND Genomic variant prioritisation is one of the most significant bottlenecks to mainstream genomic testing in healthcare. Tools to improve precision while ensuring high recall are critical to successful mainstream clinical genomic testing, in particular for whole genome sequencing where millions of variants must be considered for each patient. METHODS We developed EyeG2P, a publicly available database and web application using the Ensembl Variant Effect Predictor. EyeG2P is tailored for efficient variant prioritisation for individuals with inherited ophthalmic conditions. We assessed the sensitivity of EyeG2P in 1234 individuals with a broad range of eye conditions who had previously received a confirmed molecular diagnosis through routine genomic diagnostic approaches. For a prospective cohort of 83 individuals, we assessed the precision of EyeG2P in comparison with routine diagnostic approaches. For 10 additional individuals, we assessed the utility of EyeG2P for whole genome analysis. RESULTS EyeG2P had 99.5% sensitivity for genomic variants previously identified as clinically relevant through routine diagnostic analysis (n=1234 individuals). Prospectively, EyeG2P enabled a significant increase in precision (35% on average) in comparison with routine testing strategies (p<0.001). We demonstrate that incorporation of EyeG2P into whole genome sequencing analysis strategies can reduce the number of variants for analysis to six variants, on average, while maintaining high diagnostic yield. CONCLUSION Automated filtering of genomic variants through EyeG2P can increase the efficiency of diagnostic testing for individuals with a broad range of inherited ophthalmic disorders.
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Affiliation(s)
- Eva Lenassi
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Ana Carvalho
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Medical Genetic Unit, Pediatric Hospital, Coimbra Hospital and Universitary Centre (CHUC), Coimbra, Portugal
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | | | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Tracy Fletcher
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Claire Hardcastle
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | | | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | | | - Panagiotis I Sergouniotis
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Michel Michaelides
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Andrew Webster
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Simon C Ramsden
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | | | - David R Fitzpatrick
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Graeme C Black
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Jamie M Ellingford
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Genomics England Ltd, London, UK
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Ruiz-Ceja KA, Capasso D, Pinelli M, Del Prete E, Carrella D, di Bernardo D, Banfi S. Definition of the transcriptional units of inherited retinal disease genes by meta-analysis of human retinal transcriptome data. BMC Genomics 2023; 24:206. [PMID: 37072692 PMCID: PMC10111803 DOI: 10.1186/s12864-023-09300-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 04/07/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Inherited retinal diseases (IRD) are genetically heterogeneous disorders that cause the dysfunction or loss of photoreceptor cells and ultimately lead to blindness. To date, next-generation sequencing procedures fail to detect pathogenic sequence variants in coding regions of known IRD disease genes in about 30-40% of patients. One of the possible explanations for this missing heritability is the presence of yet unidentified transcripts of known IRD genes. Here, we aimed to define the transcript composition of IRD genes in the human retina by a meta-analysis of publicly available RNA-seq datasets using an ad-hoc designed pipeline. RESULTS We analysed 218 IRD genes and identified 5,054 transcripts, 3,367 of which were not previously reported. We assessed their putative expression levels and focused our attention on 435 transcripts predicted to account for at least 5% of the expression of the corresponding gene. We looked at the possible impact of the newly identified transcripts at the protein level and experimentally validated a subset of them. CONCLUSIONS This study provides an unprecedented, detailed overview of the complexity of the human retinal transcriptome that can be instrumental in contributing to the resolution of some cases of missing heritability in IRD patients.
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Affiliation(s)
- Karla Alejandra Ruiz-Ceja
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078, Pozzuoli, Italy
- Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Program in Molecular Life Science, University of Campania "Luigi Vanvitelli", Via Vivaldi, 43, 81100, Caserta, Italy
| | - Dalila Capasso
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078, Pozzuoli, Italy
- Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomic and Experimental Medicine Program, University of Naples "Federico II", Largo S. Marcellino, 10, 80138, Napoli, Italy
| | - Michele Pinelli
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078, Pozzuoli, Italy
| | - Eugenio Del Prete
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078, Pozzuoli, Italy
| | - Diego Carrella
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078, Pozzuoli, Italy
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078, Pozzuoli, Italy
- Chemical Engineering, University of Naples "Federico II", Piazzale Tecchio, 80, 80125, Napoli, Italy
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei, 34, 80078, Pozzuoli, Italy.
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via de Crecchio, 7, 80138, Napoli, Italy.
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8
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Wang X, You B, Yin F, Chen C, He H, Liu F, Pan Z, Ni X, Pang N, Peng J. A presumed missense variant in the U2AF2 gene causes exon skipping in neurodevelopmental diseases. J Hum Genet 2023; 68:375-382. [PMID: 36747105 DOI: 10.1038/s10038-023-01128-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/14/2022] [Accepted: 01/23/2023] [Indexed: 02/08/2023]
Abstract
U2 small nuclear RNA auxiliary factor 2 (U2AF2) is an indispensable pre-mRNA splicing factor in the early process of splicing. Recently, U2AF2 was reported as a novel candidate gene associated with neurodevelopmental disorders. Herein, we report a patient with a novel presumed heterozygous missense variant in the U2AF2 gene (c.603G>T), who has a similar clinical phenotype as the patient reported before, including epilepsy, intellectual disability, language delay, microcephaly, and hypoplastic corpus callosum. We reviewed the phenotypic and genetic spectrum of patients with U2AF2-related neurological diseases, both newly diagnosed and previously reported. To investigate the possible pathogenesis, EBV-immortalized lymphoblastoid cells were derived from the peripheral blood obtained from the patient and control groups. Furthermore, according to the results of WB, RT-PCR, Q-PCR, and cDNA sequencing of RT-PCR products, the presumed missense variant c.603G>T caused exon 6 skipping in the U2AF2 mRNA transcript and led to a truncated protein (p.E163_E201del). Cell Counting Kit-8 (CCK-8) and cell cycle detection demonstrated that the variant c.603G>T inhibited the proliferation of patient lymphocyte cells compared with the control group. This study is aimed at expanding the phenotypic and genetic spectrum of U2AF2-related neurodevelopmental diseases and investigating the potential effects. This is the first report of the possible pathogenesis of a U2AF2 gene pathogenic variant in a patient with neurodevelopmental diseases and shows that a novel presumed missense variant in the U2AF2 gene causes exon skipping.
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Affiliation(s)
- Xiaole Wang
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Baiyang You
- Department of Physical Medicine & Rehabilitation, Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, Hunan Province, China.,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Changsha, China
| | - Chen Chen
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Hailan He
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Fangyun Liu
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Zou Pan
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Xiaoyuan Ni
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Nan Pang
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, Hunan Province, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital of Central South University, Changsha, Hunan Province, China. .,Clinical Research Center for Children Neurodevelopmental Disabilities of Hunan Province, Changsha, China.
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9
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Skryabin NA, Zhigalina DI, Stepanov VA. The Role of Splicing in the Pathogenesis of Monogenic Diseases. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422100088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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10
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Ellingford JM, Ahn JW, Bagnall RD, Baralle D, Barton S, Campbell C, Downes K, Ellard S, Duff-Farrier C, FitzPatrick DR, Greally JM, Ingles J, Krishnan N, Lord J, Martin HC, Newman WG, O’Donnell-Luria A, Ramsden SC, Rehm HL, Richardson E, Singer-Berk M, Taylor JC, Williams M, Wood JC, Wright CF, Harrison SM, Whiffin N. Recommendations for clinical interpretation of variants found in non-coding regions of the genome. Genome Med 2022; 14:73. [PMID: 35850704 PMCID: PMC9295495 DOI: 10.1186/s13073-022-01073-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/16/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND The majority of clinical genetic testing focuses almost exclusively on regions of the genome that directly encode proteins. The important role of variants in non-coding regions in penetrant disease is, however, increasingly being demonstrated, and the use of whole genome sequencing in clinical diagnostic settings is rising across a large range of genetic disorders. Despite this, there is no existing guidance on how current guidelines designed primarily for variants in protein-coding regions should be adapted for variants identified in other genomic contexts. METHODS We convened a panel of nine clinical and research scientists with wide-ranging expertise in clinical variant interpretation, with specific experience in variants within non-coding regions. This panel discussed and refined an initial draft of the guidelines which were then extensively tested and reviewed by external groups. RESULTS We discuss considerations specifically for variants in non-coding regions of the genome. We outline how to define candidate regulatory elements, highlight examples of mechanisms through which non-coding region variants can lead to penetrant monogenic disease, and outline how existing guidelines can be adapted for the interpretation of these variants. CONCLUSIONS These recommendations aim to increase the number and range of non-coding region variants that can be clinically interpreted, which, together with a compatible phenotype, can lead to new diagnoses and catalyse the discovery of novel disease mechanisms.
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Affiliation(s)
- Jamie M. Ellingford
- grid.5379.80000000121662407Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, M13 9PT UK ,grid.498924.a0000 0004 0430 9101Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL UK ,grid.498322.6Genomics England, London, UK
| | - Joo Wook Ahn
- grid.24029.3d0000 0004 0383 8386Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Richard D. Bagnall
- grid.1013.30000 0004 1936 834XAgnes Ginges Centre for Molecular Cardiology at Centenary Institute, University of Sydney, Sydney, Australia
| | - Diana Baralle
- grid.5491.90000 0004 1936 9297School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK ,grid.430506.40000 0004 0465 4079Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Stephanie Barton
- grid.498924.a0000 0004 0430 9101Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL UK
| | - Chris Campbell
- grid.498924.a0000 0004 0430 9101Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL UK
| | - Kate Downes
- grid.24029.3d0000 0004 0383 8386Cambridge Genomics Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Sian Ellard
- grid.8391.30000 0004 1936 8024Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK ,grid.419309.60000 0004 0495 6261South West Genomic Laboratory Hub, Exeter Genomic Laboratory, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Celia Duff-Farrier
- grid.418484.50000 0004 0380 7221South West NHS Genomic Laboratory Hub, Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - David R. FitzPatrick
- grid.417068.c0000 0004 0624 9907MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - John M. Greally
- grid.251993.50000000121791997Department of Pediatrics, Division of Pediatric Genetic, Medicine, Children’s Hospital at Montefiore/Montefiore Medical Center/Albert, Einstein College of Medicine, Bronx, NY USA
| | - Jodie Ingles
- grid.1005.40000 0004 4902 0432Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia ,grid.1058.c0000 0000 9442 535XCentre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Neesha Krishnan
- grid.1005.40000 0004 4902 0432Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia ,grid.1058.c0000 0000 9442 535XCentre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Jenny Lord
- grid.5491.90000 0004 1936 9297School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Hilary C. Martin
- grid.10306.340000 0004 0606 5382Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - William G. Newman
- grid.5379.80000000121662407Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicines and Health, University of Manchester, Manchester, M13 9PT UK ,grid.498924.a0000 0004 0430 9101Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL UK
| | - Anne O’Donnell-Luria
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.2515.30000 0004 0378 8438Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA USA ,grid.32224.350000 0004 0386 9924Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA USA
| | - Simon C. Ramsden
- grid.498924.a0000 0004 0430 9101Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, M13 9WL UK
| | - Heidi L. Rehm
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.32224.350000 0004 0386 9924Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA USA
| | - Ebony Richardson
- grid.1005.40000 0004 4902 0432Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, Australia ,grid.1058.c0000 0000 9442 535XCentre for Population Genomics, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Moriel Singer-Berk
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Jenny C. Taylor
- grid.4991.50000 0004 1936 8948National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK ,grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Maggie Williams
- grid.418484.50000 0004 0380 7221South West NHS Genomic Laboratory Hub, Bristol Genetics Laboratory, North Bristol NHS Trust, Bristol, UK
| | - Jordan C. Wood
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Caroline F. Wright
- grid.8391.30000 0004 1936 8024Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Steven M. Harrison
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.465138.d0000 0004 0455 211XAmbry Genetics, Aliso Viejo, CA USA
| | - Nicola Whiffin
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.4991.50000 0004 1936 8948Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
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11
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Tian L, Chen C, Song Y, Zhang X, Xu K, Xie Y, Jin ZB, Li Y. Phenotype-Based Genetic Analysis Reveals Missing Heritability of ABCA4-Related Retinopathy: Deep Intronic Variants and Copy Number Variations. Invest Ophthalmol Vis Sci 2022; 63:5. [PMID: 35657619 PMCID: PMC9185996 DOI: 10.1167/iovs.63.6.5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Purpose To identify the missing heritability of ABCA4-related retinopathy in a Chinese cohort. Methods We recruited 33 unrelated patients with ABCA4-related retinopathy carrying a monoallelic variant in ABCA4. All patients underwent ophthalmic examinations. Next-generation sequencing of the whole ABCA4 sequence, including coding and noncoding regions, was performed to detect deep intronic variants (DIVs) and copy number variations (CNVs). Results We identified eight missing pathogenic ABCA4 variants in 60.6% of the patients (20/33), which comprised five DIVs and three CNVs. The five DIVs, including four novel (c.1555-816T>G, c.2919-169T>G, c.2919-884G>T, and c.5461-1321A>G) and one reported (c.4539+1100A>G), accounted for the missing alleles in 51.5% of the patients. Minigene assays showed that four novel DIVs activated cryptic splice sites leading to the insertions of pseudoexons. The three novel CNVs consisted of one gross deletion of 1273 bp (exon 2) and two gross duplications covering 25.2 kb (exons 28-43) and 9.4 kb (exons 38-44). The microhomology domains were identified at the breakpoints and revealed the potential mechanisms of CNV formation. Conclusions DIVs and CNVs explained approximately two-thirds of the unresolved Chinese cases with ABCA4-related retinopathy. Combining results from phenotypic-directed screening, targeting the whole ABCA4 sequencing and in silico tools can help to identify the missing heritability.
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Affiliation(s)
- Lu Tian
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Chunjie Chen
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Yuning Song
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Xiaohui Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Ke Xu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Yue Xie
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Zi-Bing Jin
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Yang Li
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
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12
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Fadaie Z, Whelan L, Ben-Yosef T, Dockery A, Corradi Z, Gilissen C, Haer-Wigman L, Corominas J, Astuti GDN, de Rooij L, van den Born LI, Klaver CCW, Hoyng CB, Wynne N, Duignan ES, Kenna PF, Cremers FPM, Farrar GJ, Roosing S. Whole genome sequencing and in vitro splice assays reveal genetic causes for inherited retinal diseases. NPJ Genom Med 2021; 6:97. [PMID: 34795310 PMCID: PMC8602293 DOI: 10.1038/s41525-021-00261-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/21/2021] [Indexed: 01/08/2023] Open
Abstract
Inherited retinal diseases (IRDs) are a major cause of visual impairment. These clinically heterogeneous disorders are caused by pathogenic variants in more than 270 genes. As 30-40% of cases remain genetically unexplained following conventional genetic testing, we aimed to obtain a genetic diagnosis in an IRD cohort in which the genetic cause was not found using whole-exome sequencing or targeted capture sequencing. We performed whole-genome sequencing (WGS) to identify causative variants in 100 unresolved cases. After initial prioritization, we performed an in-depth interrogation of all noncoding and structural variants in genes when one candidate variant was detected. In addition, functional analysis of putative splice-altering variants was performed using in vitro splice assays. We identified the genetic cause of the disease in 24 patients. Causative coding variants were observed in genes such as ATXN7, CEP78, EYS, FAM161A, and HGSNAT. Gene disrupting structural variants were also detected in ATXN7, PRPF31, and RPGRIP1. In 14 monoallelic cases, we prioritized candidate noncanonical splice sites or deep-intronic variants that were predicted to disrupt the splicing process based on in silico analyses. Of these, seven cases were resolved as they carried pathogenic splice defects. WGS is a powerful tool to identify causative variants residing outside coding regions or heterozygous structural variants. This approach was most efficient in cases with a distinct clinical diagnosis. In addition, in vitro splice assays provide important evidence of the pathogenicity of rare variants.
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Affiliation(s)
- Zeinab Fadaie
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Laura Whelan
- The School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Tamar Ben-Yosef
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Adrian Dockery
- The School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jordi Corominas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute of Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Galuh D N Astuti
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Division of Human Genetics, Center for Biomedical Research (CEBIOR), Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Laura de Rooij
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carel B Hoyng
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Niamh Wynne
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin, Ireland
| | - Emma S Duignan
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin, Ireland
| | - Paul F Kenna
- The School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Department of Ophthalmology, Royal Victoria Eye and Ear Hospital, Dublin, Ireland
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - G Jane Farrar
- The School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
- Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands.
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13
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Rowlands C, Thomas HB, Lord J, Wai HA, Arno G, Beaman G, Sergouniotis P, Gomes-Silva B, Campbell C, Gossan N, Hardcastle C, Webb K, O'Callaghan C, Hirst RA, Ramsden S, Jones E, Clayton-Smith J, Webster AR, Douglas AGL, O'Keefe RT, Newman WG, Baralle D, Black GCM, Ellingford JM. Comparison of in silico strategies to prioritize rare genomic variants impacting RNA splicing for the diagnosis of genomic disorders. Sci Rep 2021; 11:20607. [PMID: 34663891 PMCID: PMC8523691 DOI: 10.1038/s41598-021-99747-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 09/13/2021] [Indexed: 12/22/2022] Open
Abstract
The development of computational methods to assess pathogenicity of pre-messenger RNA splicing variants is critical for diagnosis of human disease. We assessed the capability of eight algorithms, and a consensus approach, to prioritize 249 variants of uncertain significance (VUSs) that underwent splicing functional analyses. The capability of algorithms to differentiate VUSs away from the immediate splice site as being 'pathogenic' or 'benign' is likely to have substantial impact on diagnostic testing. We show that SpliceAI is the best single strategy in this regard, but that combined usage of tools using a weighted approach can increase accuracy further. We incorporated prioritization strategies alongside diagnostic testing for rare disorders. We show that 15% of 2783 referred individuals carry rare variants expected to impact splicing that were not initially identified as 'pathogenic' or 'likely pathogenic'; one in five of these cases could lead to new or refined diagnoses.
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Affiliation(s)
- Charlie Rowlands
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, 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, UK
| | - Huw B Thomas
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, 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, UK
| | - Jenny Lord
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Htoo A Wai
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Gavin Arno
- Institute of Ophthalmology, UCL, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Glenda Beaman
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, 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, UK
| | - Panagiotis Sergouniotis
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, 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, UK
| | - Beatriz Gomes-Silva
- 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, UK
| | - Christopher Campbell
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
| | - Nicole Gossan
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
| | - Claire Hardcastle
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
| | - Kevin Webb
- Manchester Adult Cystic Fibrosis Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Christopher O'Callaghan
- Respiratory, Critical Care and Anaesthesia, UCL Great Ormond Street Institute of Child Health & Great Ormond Street Children's Hospital & NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
- Centre for PCD Diagnosis and Research, Department of Infection, Immunity and Inflammation, RKCSB, University of Leicester, Leicester, UK
| | - Robert A Hirst
- Centre for PCD Diagnosis and Research, Department of Infection, Immunity and Inflammation, RKCSB, University of Leicester, Leicester, UK
| | - Simon Ramsden
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
| | - Elizabeth Jones
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
| | - Jill Clayton-Smith
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, 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, UK
| | - Andrew R Webster
- Institute of Ophthalmology, UCL, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Andrew G L Douglas
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Raymond T O'Keefe
- 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, UK
| | - William G Newman
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, 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, UK
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Graeme C M Black
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, 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, UK.
| | - Jamie M Ellingford
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, 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, UK.
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14
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Functional Evaluation of Splicing for Variants of Uncertain Significance in Patients with Inherited Retinal Diseases. Genes (Basel) 2021; 12:genes12070993. [PMID: 34209753 PMCID: PMC8303747 DOI: 10.3390/genes12070993] [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: 06/08/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 01/13/2023] Open
Abstract
Inherited retinal diseases (IRD) comprise a heterogeneous set of clinical and genetic disorders that lead to blindness. Given the emerging opportunities in precision medicine and gene therapy, it has become increasingly important to determine whether DNA variants with uncertain significance (VUS) are responsible for patients’ IRD. This research was performed to assess the functional consequence of six VUS identified in patients with IRD. Clinical assessments included an ophthalmic examination, best-corrected visual acuity, and kinetic perimetry. Imaging was acquired with the Optos ultra-widefield camera and spectral domain optical coherence tomography (SD-OCT). Genetic testing was performed by Molecular Vision Laboratories. VUS that were predicted to alter splicing were analyzed with a minigene assay, which revealed that VUS in the genes OPA1, CNGB1, and CLUAP1 altered spicing mechanisms. Due to emerging gene and cell therapies, these results expand the genotype-phenotype correlations for patients diagnosed with an IRD.
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15
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Truty R, Ouyang K, Rojahn S, Garcia S, Colavin A, Hamlington B, Freivogel M, Nussbaum RL, Nykamp K, Aradhya S. Spectrum of splicing variants in disease genes and the ability of RNA analysis to reduce uncertainty in clinical interpretation. Am J Hum Genet 2021; 108:696-708. [PMID: 33743207 PMCID: PMC8059334 DOI: 10.1016/j.ajhg.2021.03.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/02/2021] [Indexed: 12/20/2022] Open
Abstract
The complexities of gene expression pose challenges for the clinical interpretation of splicing variants. To better understand splicing variants and their contribution to hereditary disease, we evaluated their prevalence, clinical classifications, and associations with diseases, inheritance, and functional characteristics in a 689,321-person clinical cohort and two large public datasets. In the clinical cohort, splicing variants represented 13% of all variants classified as pathogenic (P), likely pathogenic (LP), or variants of uncertain significance (VUSs). Most splicing variants were outside essential splice sites and were classified as VUSs. Among all individuals tested, 5.4% had a splicing VUS. If RNA analysis were to contribute supporting evidence to variant interpretation, we estimated that splicing VUSs would be reclassified in 1.7% of individuals in our cohort. This would result in a clinically significant result (i.e., P/LP) in 0.1% of individuals overall because most reclassifications would change VUSs to likely benign. In ClinVar, splicing VUSs were 4.8% of reported variants and could benefit from RNA analysis. In the Genome Aggregation Database (gnomAD), splicing variants comprised 9.4% of variants in protein-coding genes; most were rare, precluding unambiguous classification as benign. Splicing variants were depleted in genes associated with dominant inheritance and haploinsufficiency, although some genes had rare variants at essential splice sites or had common splicing variants that were most likely compatible with normal gene function. Overall, we describe the contribution of splicing variants to hereditary disease, the potential utility of RNA analysis for reclassifying splicing VUSs, and how natural variation may confound clinical interpretation of splicing variants.
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Affiliation(s)
| | - Karen Ouyang
- Invitae, 1400 16th St, San Francisco, CA 94103, USA
| | - Susan Rojahn
- Invitae, 1400 16th St, San Francisco, CA 94103, USA
| | - Sarah Garcia
- Invitae, 1400 16th St, San Francisco, CA 94103, USA
| | | | | | | | | | - Keith Nykamp
- Invitae, 1400 16th St, San Francisco, CA 94103, USA
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16
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Tarilonte M, Ramos P, Moya J, Fernandez-Sanz G, Blanco-Kelly F, Swafiri ST, Villaverde C, Romero R, Tamayo A, Gener B, Calvas P, Ayuso C, Corton M. Activation of cryptic donor splice sites by non-coding and coding PAX6 variants contributes to congenital aniridia. J Med Genet 2021; 59:428-437. [PMID: 33782094 DOI: 10.1136/jmedgenet-2020-106932] [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] [Received: 02/20/2020] [Revised: 01/22/2021] [Accepted: 02/14/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND The paired-domain transcription factor paired box gene 6 (PAX6) causes a wide spectrum of ocular developmental anomalies, including congenital aniridia, Peters anomaly and microphthalmia. Here, we aimed to functionally assess the involvement of seven potentially non-canonical splicing variants on missplicing of exon 6, which represents the main hotspot region for loss-of-function PAX6 variants. METHODS By locus-specific analysis of PAX6 using Sanger and/or targeted next-generation sequencing, we screened a Spanish cohort of 106 patients with PAX6-related diseases. Functional splicing assays were performed by in vitro minigene approaches or directly in RNA from patient-derived lymphocytes cell line, when available. RESULTS Five out seven variants, including three synonymous changes, one small exonic deletion and one non-canonical splice variant, showed anomalous splicing patterns yielding partial exon skipping and/or elongation. CONCLUSION We describe new spliceogenic mechanisms for PAX6 variants mediated by creating or strengthening five different cryptic donor sites at exon 6. Our work revealed that the activation of cryptic PAX6 splicing sites seems to be a recurrent and underestimated cause of aniridia. Our findings pointed out the importance of functional assessment of apparently silent PAX6 variants to uncover hidden genetic alterations and to improve variant interpretation for genetic counselling in aniridia.
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Affiliation(s)
- Maria Tarilonte
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria - Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD-UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Patricia Ramos
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria - Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD-UAM), Madrid, Spain
| | - Jennifer Moya
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria - Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD-UAM), Madrid, Spain
| | - Guilermo Fernandez-Sanz
- Department of Ophthalmology, Fundación Jiménez Díaz University Hospital, Madrid, Spain.,Department of Ophthalmology, Clínica Universidad de Navarra, Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria - Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD-UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Saoud Tahsin Swafiri
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria - Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD-UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Cristina Villaverde
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria - Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD-UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Raquel Romero
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria - Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD-UAM), Madrid, Spain
| | - Alejandra Tamayo
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria - Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD-UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Blanca Gener
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain.,Department of Genetics, Cruces University Hospital, BioCruces Health Research Institute, Barakaldo, Spain
| | - Patrick Calvas
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France.,INSERM U1056, Université Toulouse III, Toulouse, France
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria - Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD-UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Marta Corton
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria - Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD-UAM), Madrid, Spain .,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
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17
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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 2020; 61:36. [PMID: 32881472 PMCID: PMC7443117 DOI: 10.1167/iovs.61.10.36] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/16/2020] [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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