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Lin S, Schiff E, Arno G, Mahroo OA, Webster AR. Unveiling hidden genetic complexity: Coexistence of HGSNAT and EYS variants in a patient with retinal dystrophy. Am J Med Genet A 2024:e63805. [PMID: 38988050 DOI: 10.1002/ajmg.a.63805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 07/12/2024]
Affiliation(s)
- Siying Lin
- National Institute of Health Research Biomedical Research Centre, Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Elena Schiff
- National Institute of Health Research Biomedical Research Centre, Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Gavin Arno
- National Institute of Health Research Biomedical Research Centre, Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
- Division of Research, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Omar A Mahroo
- National Institute of Health Research Biomedical Research Centre, Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Ophthalmology, St Thomas' Hospital, London, UK
| | - Andrew R Webster
- National Institute of Health Research Biomedical Research Centre, Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
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Lin S, Vermeirsch S, Pontikos N, Martin-Gutierrez MP, Daich Varela M, Malka S, Schiff E, Knight H, Wright G, Jurkute N, Simcoe MJ, Yu-Wai-Man P, Moosajee M, Michaelides M, Mahroo OA, Webster AR, Arno G. Spectrum of Genetic Variants in the Most Common Genes Causing Inherited Retinal Disease in a Large Molecularly Characterized United Kingdom Cohort. Ophthalmol Retina 2024; 8:699-709. [PMID: 38219857 DOI: 10.1016/j.oret.2024.01.012] [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: 09/14/2023] [Revised: 12/12/2023] [Accepted: 01/08/2024] [Indexed: 01/16/2024]
Abstract
PURPOSE Inherited retinal disease (IRD) is a leading cause of blindness. Recent advances in gene-directed therapies highlight the importance of understanding the genetic basis of these disorders. This study details the molecular spectrum in a large United Kingdom (UK) IRD patient cohort. DESIGN Retrospective study of electronic patient records. PARTICIPANTS Patients with IRD who attended the Genetics Service at Moorfields Eye Hospital between 2003 and July 2020, in whom a molecular diagnosis was identified. METHODS Genetic testing was undertaken via a combination of single-gene testing, gene panel testing, whole exome sequencing, and more recently, whole genome sequencing. Likely disease-causing variants were identified from entries within the genetics module of the hospital electronic patient record (OpenEyes Electronic Medical Record). Analysis was restricted to only genes listed in the Genomics England PanelApp R32 Retinal Disorders panel (version 3.24), which includes 412 genes associated with IRD. Manual curation ensured consistent variant annotation and included only plausible disease-associated variants. MAIN OUTCOME MEASURES Detailed analysis was performed for variants in the 5 most frequent genes (ABCA4, USH2A, RPGR, PRPH2, and BEST1), as well as for the most common variants encountered in the IRD study cohort. RESULTS We identified 4415 individuals from 3953 families with molecularly diagnosed IRD (variants in 166 genes). Of the families, 42.7% had variants in 1 of the 5 most common IRD genes. Complex disease alleles contributed to disease in 16.9% of affected families with ABCA4-associated retinopathy. USH2A exon 13 variants were identified in 43% of affected individuals with USH2A-associated IRD. Of the RPGR variants, 71% were clustered in the ORF15 region. PRPH2 and BEST1 variants were associated with a range of dominant and recessive IRD phenotypes. Of the 20 most prevalent variants identified, 5 were not in the most common genes; these included founder variants in CNGB3, BBS1, TIMP3, EFEMP1, and RP1. CONCLUSIONS We describe the most common pathogenic IRD alleles in a large single-center multiethnic UK cohort and the burden of disease, in terms of families affected, attributable to these variants. Our findings will inform IRD diagnoses in future patients and help delineate the cohort of patients eligible for gene-directed therapies under development. FINANCIAL DISCLOSURE(S) Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Siying Lin
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Sandra Vermeirsch
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom
| | - Nikolas Pontikos
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Maria Pilar Martin-Gutierrez
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom
| | - Malena Daich Varela
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Samantha Malka
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Elena Schiff
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Hannah Knight
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Genevieve Wright
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Neringa Jurkute
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom; Department of Neuro-Ophhalmology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Mark J Simcoe
- UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Patrick Yu-Wai-Man
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Mariya Moosajee
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Michel Michaelides
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Omar A Mahroo
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom; Department of Ophthalmology, St Thomas' Hospital, London, United Kingdom
| | - Andrew R Webster
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom
| | - Gavin Arno
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the UCL Institute of Ophthalmology, London, United Kingdom; UCL Institute of Ophthalmology, University College London, United Kingdom.
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Ba-Abbad R. Revisiting molecular diagnosis in a family with retinitis pigmentosa: integrating deep phenotyping and bioinformatic analysis. Ophthalmic Genet 2024:1-4. [PMID: 38767358 DOI: 10.1080/13816810.2024.2352377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Affiliation(s)
- Rola Ba-Abbad
- Retina Division, Ocular Genetics Services, King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
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Wang B, Wang M, Lin Y, Zhao J, Gu H, Li X. Circulating tumor DNA methylation: a promising clinical tool for cancer diagnosis and management. Clin Chem Lab Med 2024; 0:cclm-2023-1327. [PMID: 38443752 DOI: 10.1515/cclm-2023-1327] [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: 11/23/2023] [Accepted: 02/19/2024] [Indexed: 03/07/2024]
Abstract
Cancer continues to pose significant challenges to the medical community. Early detection, accurate molecular profiling, and adequate assessment of treatment response are critical factors in improving the quality of life and survival of cancer patients. Accumulating evidence shows that circulating tumor DNA (ctDNA) shed by tumors into the peripheral blood preserves the genetic and epigenetic information of primary tumors. Notably, DNA methylation, an essential and stable epigenetic modification, exhibits both cancer- and tissue-specific patterns. As a result, ctDNA methylation has emerged as a promising molecular marker for noninvasive testing in cancer clinics. In this review, we summarize the existing techniques for ctDNA methylation detection, describe the current research status of ctDNA methylation, and present the potential applications of ctDNA-based assays in the clinic. The insights presented in this article could serve as a roadmap for future research and clinical applications of ctDNA methylation.
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Affiliation(s)
- Binliang Wang
- Department of Respiratory Medicine, Huangyan Hospital Affiliated to Wenzhou Medical University, Taizhou, P.R. China
| | - Meng Wang
- Institute of Health Education, Hangzhou Center for Disease Control and Prevention, Hangzhou, P.R. China
| | - Ya Lin
- Zhejiang University of Chinese Medicine, Hangzhou, P.R. China
| | - Jinlan Zhao
- Scientific Research Department, Zhejiang Shengting Medical Company, Hangzhou, P.R. China
| | - Hongcang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, P.R. China
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, P.R. China
| | - Xiangjuan Li
- Department of Gynaecology, Hangzhou Obstetrics and Gynecology Hospital, Hangzhou, P.R. China
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Lofaro FD, Mucciolo DP, Murro V, Pavese L, Quaglino D, Boraldi F. A Case Report of Pseudoxanthoma Elasticum with Rare Sequence Variants in Genes Related to Inherited Retinal Diseases. Diagnostics (Basel) 2021; 11:diagnostics11101800. [PMID: 34679498 PMCID: PMC8534466 DOI: 10.3390/diagnostics11101800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/17/2021] [Accepted: 09/27/2021] [Indexed: 01/11/2023] Open
Abstract
A case of a patient with an early and severe visual impairment is described. Due to the occurrence of skin papules a suspect of pseudoxanthoma elasticum (PXE) was posed. PXE is a rare autosomal recessive disease clinically characterized by skin, cardiovascular and ocular manifestations, these last being those that most severely affect patients’ quality of life. A whole exome sequencing approach focusing on 340 genes related to the calcification process and/or to inherited retinal diseases (IRDs) was performed. Rare monoallelic sequence variants in ABCA4, ABCC6, IMPG1, POC1B and RAX2 were found. The presence of calcified elastic fibers was assessed by ultrastructural analysis on a skin biopsy. Diagnosis of PXE was based on clinical, biomolecular and morphological results, although the additional involvement of several IRD genes is important to explain the unexpectedly severe ophthalmological phenotype of the patient also in prognostic and therapeutic perspectives. Data indicate that genetic screening using a wide-spectrum analysis approach is essential to assist ophthalmologists in improving patient counseling.
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Affiliation(s)
- Francesco Demetrio Lofaro
- Department of Life Science, University of Modena and Reggio Emilia, 41125 Modena, Italy; (F.D.L.); (D.Q.)
| | - Dario Pasquale Mucciolo
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Eye Clinic, 50139 Florence, Italy; (D.P.M.); (V.M.); (L.P.)
| | - Vittoria Murro
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Eye Clinic, 50139 Florence, Italy; (D.P.M.); (V.M.); (L.P.)
| | - Laura Pavese
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Eye Clinic, 50139 Florence, Italy; (D.P.M.); (V.M.); (L.P.)
| | - Daniela Quaglino
- Department of Life Science, University of Modena and Reggio Emilia, 41125 Modena, Italy; (F.D.L.); (D.Q.)
| | - Federica Boraldi
- Department of Life Science, University of Modena and Reggio Emilia, 41125 Modena, Italy; (F.D.L.); (D.Q.)
- Correspondence:
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Lofaro FD, Mucciolo DP, Murro V, Pavese L, Quaglino D, Boraldi F. From Clinical Diagnosis to the Discovery of Multigene Rare Sequence Variants in Pseudoxanthoma elasticum: A Case Report. Front Med (Lausanne) 2021; 8:726856. [PMID: 34513887 PMCID: PMC8427021 DOI: 10.3389/fmed.2021.726856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 07/30/2021] [Indexed: 12/03/2022] Open
Abstract
Pseudoxanthoma elasticum (PXE) is a rare autosomal recessive disease clinically characterised by early cutaneous alterations, and by late clinically relevant ocular, and cardiovascular manifestations. ABCC6 genetic tests are used to confirm clinical PXE diagnosis, but this strategy may be rather challenging when only one ABCC6 pathogenic variant is found. A next-generation sequencing approach focusing on 362 genes related to the calcification process and/or to inherited retinal diseases was performed on a patient with clinical PXE diagnosis (skin papules and laxity, angioid streaks, and atrophy) who was carrier of only one ABCC6 rare sequence variant. Beside ABCC6, several rare sequence variants were detected which can contribute either to the occurrence of calcification (GGCX and SERPINF1 genes) and/or to ophthalmological manifestations (ABCA4, AGBL5, CLUAP1, and KCNV2 genes). This wide-spectrum analysis approach facilitates the identification of rare variants possibly involved in PXE, thus avoiding invasive skin biopsy as well as expensive and time-consuming diagnostic odyssey and allows to broaden and to deepen the knowledge on this complex rare disease and to improve patients' counselling, also with a future perspective of personalised medicine.
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Affiliation(s)
| | - Dario Pasquale Mucciolo
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Eye Clinic, Florence, Italy
| | - Vittoria Murro
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Eye Clinic, Florence, Italy
| | - Laura Pavese
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Eye Clinic, Florence, Italy
| | - Daniela Quaglino
- Department of Life Science, University of Modena and Reggio Emilia, Modena, Italy
| | - Federica Boraldi
- Department of Life Science, University of Modena and Reggio Emilia, Modena, Italy
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