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Hamvas A, Chaudhari BP, Nogee LM. Genetic testing for diffuse lung diseases in children. Pediatr Pulmonol 2024; 59:2286-2297. [PMID: 37191361 DOI: 10.1002/ppul.26447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/04/2023] [Accepted: 04/23/2023] [Indexed: 05/17/2023]
Abstract
Newly developing genomic technologies are an increasingly important part of clinical care and thus, it is not only important to understand the technologies and their limitations, but to also interpret the findings in an actionable fashion. Clinical geneticists and genetic counselors are now an integral part of the clinical team and are able to bridge the complexities of this rapidly changing science between the bedside clinicians and patients. This manuscript reviews the terminology, the current technology, some of the known genetic disorders that result in lung disease, and indications for genetic testing with associated caveats. Because this field is evolving quickly, we also provide links to websites that provide continuously updated information important for integrating genomic technology results into clinical decision-making.
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Affiliation(s)
- Aaron Hamvas
- Department of Pediatrics, Division of Neonatology, Ann and Robert H. Lurie Children's Hospital of Chicago and Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Bimal P Chaudhari
- Divisions of Genetics and Genomic Medicine, Neonatology, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Lawrence M Nogee
- Department of Pediatrics, Eudowood Neonatal Pulmonary Division, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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2
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LaFlamme CW, Rastin C, Sengupta S, Pennington HE, Russ-Hall SJ, Schneider AL, Bonkowski ES, Almanza Fuerte EP, Allan TJ, Zalusky MPG, Goffena J, Gibson SB, Nyaga DM, Lieffering N, Hebbar M, Walker EV, Darnell D, Olsen SR, Kolekar P, Djekidel MN, Rosikiewicz W, McConkey H, Kerkhof J, Levy MA, Relator R, Lev D, Lerman-Sagie T, Park KL, Alders M, Cappuccio G, Chatron N, Demain L, Genevieve D, Lesca G, Roscioli T, Sanlaville D, Tedder ML, Gupta S, Jones EA, Weisz-Hubshman M, Ketkar S, Dai H, Worley KC, Rosenfeld JA, Chao HT, Neale G, Carvill GL, Wang Z, Berkovic SF, Sadleir LG, Miller DE, Scheffer IE, Sadikovic B, Mefford HC. Diagnostic utility of DNA methylation analysis in genetically unsolved pediatric epilepsies and CHD2 episignature refinement. Nat Commun 2024; 15:6524. [PMID: 39107278 PMCID: PMC11303402 DOI: 10.1038/s41467-024-50159-6] [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: 10/20/2023] [Accepted: 06/28/2024] [Indexed: 08/09/2024] Open
Abstract
Sequence-based genetic testing identifies causative variants in ~ 50% of individuals with developmental and epileptic encephalopathies (DEEs). Aberrant changes in DNA methylation are implicated in various neurodevelopmental disorders but remain unstudied in DEEs. We interrogate the diagnostic utility of genome-wide DNA methylation array analysis on peripheral blood samples from 582 individuals with genetically unsolved DEEs. We identify rare differentially methylated regions (DMRs) and explanatory episignatures to uncover causative and candidate genetic etiologies in 12 individuals. Using long-read sequencing, we identify DNA variants underlying rare DMRs, including one balanced translocation, three CG-rich repeat expansions, and four copy number variants. We also identify pathogenic variants associated with episignatures. Finally, we refine the CHD2 episignature using an 850 K methylation array and bisulfite sequencing to investigate potential insights into CHD2 pathophysiology. Our study demonstrates the diagnostic yield of genome-wide DNA methylation analysis to identify causal and candidate variants as 2% (12/582) for unsolved DEE cases.
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Affiliation(s)
- Christy W LaFlamme
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Cassandra Rastin
- Department of Pathology & Laboratory Medicine, Western University, London, ON, N5A 3K7, Canada
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Soham Sengupta
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Helen E Pennington
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Mathematics & Statistics, Rhodes College, Memphis, TN, 38112, USA
| | - Sophie J Russ-Hall
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Amy L Schneider
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Emily S Bonkowski
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Edith P Almanza Fuerte
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Talia J Allan
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Miranda Perez-Galey Zalusky
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
| | - Joy Goffena
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
| | - Sophia B Gibson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Denis M Nyaga
- Department of Paediatrics and Child Health, University of Otago, Wellington, 6242, New Zealand
| | - Nico Lieffering
- Department of Paediatrics and Child Health, University of Otago, Wellington, 6242, New Zealand
| | - Malavika Hebbar
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
| | - Emily V Walker
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital Memphis, Memphis, TN, 38105, USA
| | - Daniel Darnell
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital Memphis, Memphis, TN, 38105, USA
| | - Scott R Olsen
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital Memphis, Memphis, TN, 38105, USA
| | - Pandurang Kolekar
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Mohamed Nadhir Djekidel
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Wojciech Rosikiewicz
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada
| | - Dorit Lev
- Institute of Medical Genetics, Wolfson Medical Center, Holon, 58100, Israel
| | - Tally Lerman-Sagie
- Fetal Neurology Clinic, Pediatric Neurology Unit, Wolfson Medical Center, Holon, 58100, Israel
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Kristen L Park
- Departments of Pediatrics and Neurology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Marielle Alders
- Department of Human Genetics, Amsterdam Reproduction and Development Research Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, Meibergdreef 9, Amsterdam, Netherlands
| | - Gerarda Cappuccio
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Translational Medicine, Federico II University of Naples, Naples, Italy
| | - Nicolas Chatron
- Department of Medical Genetics, Member of the ERN EpiCARE, University Hospital of Lyon and Claude Bernard Lyon I University, Lyon, France
- Pathophysiology and Genetics of Neuron and Muscle (PNMG), UCBL, CNRS UMR5261 - INSERM, U1315, Lyon, France
| | - Leigh Demain
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - David Genevieve
- Montpellier University, Inserm Unit 1183, Reference Center for Rare Diseases Developmental Anomaly and Malformative Syndrome, Clinical Genetic Department, CHU Montpellier, Montpellier, France
| | - Gaetan Lesca
- Department of Medical Genetics, Member of the ERN EpiCARE, University Hospital of Lyon and Claude Bernard Lyon I University, Lyon, France
- Pathophysiology and Genetics of Neuron and Muscle (PNMG), UCBL, CNRS UMR5261 - INSERM, U1315, Lyon, France
| | - Tony Roscioli
- Neuroscience Research Australia (NeuRA), Sydney, NSW, Australia
- Prince of Wales Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- New South Wales Health Pathology Randwick Genomics, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Damien Sanlaville
- Department of Medical Genetics, Member of the ERN EpiCARE, University Hospital of Lyon and Claude Bernard Lyon I University, Lyon, France
- Pathophysiology and Genetics of Neuron and Muscle (PNMG), UCBL, CNRS UMR5261 - INSERM, U1315, Lyon, France
| | | | - Sachin Gupta
- TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Elizabeth A Jones
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Monika Weisz-Hubshman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Texas Children's Hospital, Genetic Department, Houston, TX, 77030, USA
| | - Shamika Ketkar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hongzheng Dai
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kim C Worley
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hsiao-Tuan Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pediatrics, Section of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
- Cain Pediatric Neurology Research Foundation Laboratories, Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
- Texas Children's Hospital, Houston, TX, 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
- McNair Medical Institute, The Robert and Janice McNair Foundation, Houston, TX, 77030, USA
| | - Geoffrey Neale
- Hartwell Center for Bioinformatics and Biotechnology, St. Jude Children's Research Hospital Memphis, Memphis, TN, 38105, USA
| | - Gemma L Carvill
- Ken and Ruth Davee Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Zhaoming Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Epidemiology and Cancer Control, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago, Wellington, 6242, New Zealand
| | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC, 3084, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, VIC, Australia
- Florey Institute and Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Bekim Sadikovic
- Department of Pathology & Laboratory Medicine, Western University, London, ON, N5A 3K7, Canada.
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, N6A 5W9, Canada.
| | - Heather C Mefford
- Center for Pediatric Neurological Disease Research, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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Tanudisastro HA, Deveson IW, Dashnow H, MacArthur DG. Sequencing and characterizing short tandem repeats in the human genome. Nat Rev Genet 2024; 25:460-475. [PMID: 38366034 DOI: 10.1038/s41576-024-00692-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2023] [Indexed: 02/18/2024]
Abstract
Short tandem repeats (STRs) are highly polymorphic sequences throughout the human genome that are composed of repeated copies of a 1-6-bp motif. Over 1 million variable STR loci are known, some of which regulate gene expression and influence complex traits, such as height. Moreover, variants in at least 60 STR loci cause genetic disorders, including Huntington disease and fragile X syndrome. Accurately identifying and genotyping STR variants is challenging, in particular mapping short reads to repetitive regions and inferring expanded repeat lengths. Recent advances in sequencing technology and computational tools for STR genotyping from sequencing data promise to help overcome this challenge and solve genetically unresolved cases and the 'missing heritability' of polygenic traits. Here, we compare STR genotyping methods, analytical tools and their applications to understand the effect of STR variation on health and disease. We identify emergent opportunities to refine genotyping and quality-control approaches as well as to integrate STRs into variant-calling workflows and large cohort analyses.
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Affiliation(s)
- Hope A Tanudisastro
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia
| | - Ira W Deveson
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Harriet Dashnow
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA.
| | - Daniel G MacArthur
- Centre for Population Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.
- Faculty of Medicine and Health, University of New South Wales, Sydney, New South Wales, Australia.
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4
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Chong JX, Berger SI, Baxter S, Smith E, Xiao C, Calame DG, Hawley MH, Rivera-Munoz EA, DiTroia S, Bamshad MJ, Rehm HL. Considerations for reporting variants in novel candidate genes identified during clinical genomic testing. Genet Med 2024; 26:101199. [PMID: 38944749 DOI: 10.1016/j.gim.2024.101199] [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: 02/09/2024] [Revised: 06/18/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
Since the first novel gene discovery for a Mendelian condition was made via exome sequencing, the rapid increase in the number of genes known to underlie Mendelian conditions coupled with the adoption of exome (and more recently, genome) sequencing by diagnostic testing labs has changed the landscape of genomic testing for rare diseases. Specifically, many individuals suspected to have a Mendelian condition are now routinely offered clinical ES. This commonly results in a precise genetic diagnosis but frequently overlooks the identification of novel candidate genes. Such candidates are also less likely to be identified in the absence of large-scale gene discovery research programs. Accordingly, clinical laboratories have both the opportunity, and some might argue a responsibility, to contribute to novel gene discovery, which should, in turn, increase the diagnostic yield for many conditions. However, clinical diagnostic laboratories must necessarily balance priorities for throughput, turnaround time, cost efficiency, clinician preferences, and regulatory constraints and often do not have the infrastructure or resources to effectively participate in either clinical translational or basic genome science research efforts. For these and other reasons, many laboratories have historically refrained from broadly sharing potentially pathogenic variants in novel genes via networks such as Matchmaker Exchange, much less reporting such results to ordering providers. Efforts to report such results are further complicated by a lack of guidelines for clinical reporting and interpretation of variants in novel candidate genes. Nevertheless, there are myriad benefits for many stakeholders, including patients/families, clinicians, and researchers, if clinical laboratories systematically and routinely identify, share, and report novel candidate genes. To facilitate this change in practice, we developed criteria for triaging, sharing, and reporting novel candidate genes that are most likely to be promptly validated as underlying a Mendelian condition and translated to use in clinical settings.
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Affiliation(s)
- Jessica X Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA; Brotman-Baty Institute for Precision Medicine, Seattle, WA.
| | - Seth I Berger
- Center for Genetic Medicine Research, Children's National Research Institute, Washington, DC
| | - Samantha Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Erica Smith
- Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA
| | - Changrui Xiao
- Department of Neurology, University of California Irvine, Orange, CA
| | - Daniel G Calame
- Department of Pediatrics, Division of Pediatric Neurology and Developmental Neurosciences, Baylor College of Medicine, Houston, TX
| | | | | | - Stephanie DiTroia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Michael J Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA; Brotman-Baty Institute for Precision Medicine, Seattle, WA; Department of Pediatrics, Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
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Kingsmore SF, Nofsinger R, Ellsworth K. Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review. NPJ Genom Med 2024; 9:17. [PMID: 38413639 PMCID: PMC10899612 DOI: 10.1038/s41525-024-00404-0] [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: 10/16/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
Single locus (Mendelian) diseases are a leading cause of childhood hospitalization, intensive care unit (ICU) admission, mortality, and healthcare cost. Rapid genome sequencing (RGS), ultra-rapid genome sequencing (URGS), and rapid exome sequencing (RES) are diagnostic tests for genetic diseases for ICU patients. In 44 studies of children in ICUs with diseases of unknown etiology, 37% received a genetic diagnosis, 26% had consequent changes in management, and net healthcare costs were reduced by $14,265 per child tested by URGS, RGS, or RES. URGS outperformed RGS and RES with faster time to diagnosis, and higher rate of diagnosis and clinical utility. Diagnostic and clinical outcomes will improve as methods evolve, costs decrease, and testing is implemented within precision medicine delivery systems attuned to ICU needs. URGS, RGS, and RES are currently performed in <5% of the ~200,000 children likely to benefit annually due to lack of payor coverage, inadequate reimbursement, hospital policies, hospitalist unfamiliarity, under-recognition of possible genetic diseases, and current formatting as tests rather than as a rapid precision medicine delivery system. The gap between actual and optimal outcomes in children in ICUs is currently increasing since expanded use of URGS, RGS, and RES lags growth in those likely to benefit through new therapies. There is sufficient evidence to conclude that URGS, RGS, or RES should be considered in all children with diseases of uncertain etiology at ICU admission. Minimally, diagnostic URGS, RGS, or RES should be ordered early during admissions of critically ill infants and children with suspected genetic diseases.
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Affiliation(s)
- Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA.
| | - Russell Nofsinger
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
| | - Kasia Ellsworth
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA, USA
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Wu K, Bu F, Wu Y, Zhang G, Wang X, He S, Liu MF, Chen R, Yuan H. Exploring noncoding variants in genetic diseases: from detection to functional insights. J Genet Genomics 2024; 51:111-132. [PMID: 38181897 DOI: 10.1016/j.jgg.2024.01.001] [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: 11/05/2023] [Revised: 12/26/2023] [Accepted: 01/01/2024] [Indexed: 01/07/2024]
Abstract
Previous studies on genetic diseases predominantly focused on protein-coding variations, overlooking the vast noncoding regions in the human genome. The development of high-throughput sequencing technologies and functional genomics tools has enabled the systematic identification of functional noncoding variants. These variants can impact gene expression, regulation, and chromatin conformation, thereby contributing to disease pathogenesis. Understanding the mechanisms that underlie the impact of noncoding variants on genetic diseases is indispensable for the development of precisely targeted therapies and the implementation of personalized medicine strategies. The intricacies of noncoding regions introduce a multitude of challenges and research opportunities. In this review, we introduce a spectrum of noncoding variants involved in genetic diseases, along with research strategies and advanced technologies for their precise identification and in-depth understanding of the complexity of the noncoding genome. We will delve into the research challenges and propose potential solutions for unraveling the genetic basis of rare and complex diseases.
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Affiliation(s)
- Ke Wu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Fengxiao Bu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Yang Wu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Gen Zhang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China
| | - Xin Wang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mo-Fang Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China; State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Huijun Yuan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, Sichuan 610041, China.
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7
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Damaraju N, Miller AL, Miller DE. Long-Read DNA and RNA Sequencing to Streamline Clinical Genetic Testing and Reduce Barriers to Comprehensive Genetic Testing. J Appl Lab Med 2024; 9:138-150. [PMID: 38167773 DOI: 10.1093/jalm/jfad107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/24/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Obtaining a precise molecular diagnosis through clinical genetic testing provides information about disease prognosis or progression, allows accurate counseling about recurrence risk, and empowers individuals to benefit from precision therapies or take part in N-of-1 trials. Unfortunately, more than half of individuals with a suspected Mendelian condition remain undiagnosed after a comprehensive clinical evaluation, and the results of any individual clinical genetic test ordered during a typical evaluation may take weeks or months to return. Furthermore, commonly used technologies, such as short-read sequencing, are limited in the types of disease-causing variation they can identify. New technologies, such as long-read sequencing (LRS), are poised to solve these problems. CONTENT Recent technical advances have improved accuracy, increased throughput, and decreased the costs of commercially available LRS technologies. This has resolved many historical concerns about the use of LRS in the clinical environment and opened the door to widespread clinical adoption of LRS. Here, we review LRS technology, how it has been used in the research setting to clarify complex variants or identify disease-causing variation missed by prior clinical testing, and how it may be used clinically in the near future. SUMMARY LRS is unique in that, as a single data source, it has the potential to replace nearly every other clinical genetic test offered today. When analyzed in a stepwise fashion, LRS will simplify laboratory processes, reduce barriers to comprehensive genetic testing, increase the rate of genetic diagnoses, and shorten the amount of time required to make a molecular diagnosis.
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Affiliation(s)
- Nikhita Damaraju
- Institute for Public Health Genetics, University of Washington, Seattle, WA 98195, United States
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, United States
| | - Angela L Miller
- Department of Pediatrics, University of Washington, Seattle, WA 98195, United States
| | - Danny E Miller
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, United States
- Department of Pediatrics, University of Washington, Seattle, WA 98195, United States
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, United States
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8
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Annear DJ, Kooy RF. Unravelling the link between neurodevelopmental disorders and short tandem CGG-repeat expansions. Emerg Top Life Sci 2023; 7:265-275. [PMID: 37768318 PMCID: PMC10754333 DOI: 10.1042/etls20230021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/23/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
Neurodevelopmental disorders (NDDs) encompass a diverse group of disorders characterised by impaired cognitive abilities and developmental challenges. Short tandem repeats (STRs), repetitive DNA sequences found throughout the human genome, have emerged as potential contributors to NDDs. Specifically, the CGG trinucleotide repeat has been implicated in a wide range of NDDs, including Fragile X Syndrome (FXS), the most common inherited form of intellectual disability and autism. This review focuses on CGG STR expansions associated with NDDs and their impact on gene expression through repeat expansion-mediated epigenetic silencing. We explore the molecular mechanisms underlying CGG-repeat expansion and the resulting epigenetic modifications, such as DNA hypermethylation and gene silencing. Additionally, we discuss the involvement of other CGG STRs in neurodevelopmental diseases. Several examples, including FMR1, AFF2, AFF3, XYLT1, FRA10AC1, CBL, and DIP2B, highlight the complex relationship between CGG STR expansions and NDDs. Furthermore, recent advancements in this field are highlighted, shedding light on potential future research directions. Understanding the role of STRs, particularly CGG-repeats, in NDDs has the potential to uncover novel diagnostic and therapeutic strategies for these challenging disorders.
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Affiliation(s)
- Dale J Annear
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
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9
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Chaisson MJP, Sulovari A, Valdmanis PN, Miller DE, Eichler EE. Advances in the discovery and analyses of human tandem repeats. Emerg Top Life Sci 2023; 7:361-381. [PMID: 37905568 PMCID: PMC10806765 DOI: 10.1042/etls20230074] [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: 06/12/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023]
Abstract
Long-read sequencing platforms provide unparalleled access to the structure and composition of all classes of tandemly repeated DNA from STRs to satellite arrays. This review summarizes our current understanding of their organization within the human genome, their importance with respect to disease, as well as the advances and challenges in understanding their genetic diversity and functional effects. Novel computational methods are being developed to visualize and associate these complex patterns of human variation with disease, expression, and epigenetic differences. We predict accurate characterization of this repeat-rich form of human variation will become increasingly relevant to both basic and clinical human genetics.
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Affiliation(s)
- Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, U.S.A
- The Genomic and Epigenomic Regulation Program, USC Norris Cancer Center, University of Southern California, Los Angeles, CA 90089, U.S.A
| | - Arvis Sulovari
- Computational Biology, Cajal Neuroscience Inc, Seattle, WA 98102, U.S.A
| | - Paul N Valdmanis
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, U.S.A
| | - Danny E Miller
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, U.S.A
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, U.S.A
- Department of Pediatrics, University of Washington, Seattle, WA 98195, U.S.A
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, U.S.A
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, U.S.A
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10
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Jadhav B, Garg P, van Vugt JJFA, Ibanez K, Gagliardi D, Lee W, Shadrina M, Mokveld T, Dolzhenko E, Martin-Trujillo A, Gies SL, Rocca C, Barbosa M, Jain M, Lahiri N, Lachlan K, Houlden H, Paten B, Veldink J, Tucci A, Sharp AJ. A phenome-wide association study of methylated GC-rich repeats identifies a GCC repeat expansion in AFF3 as a significant cause of intellectual disability. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.05.03.23289461. [PMID: 37205357 PMCID: PMC10187445 DOI: 10.1101/2023.05.03.23289461] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
GC-rich tandem repeat expansions (TREs) are often associated with DNA methylation, gene silencing and folate-sensitive fragile sites and underlie several congenital and late-onset disorders. Through a combination of DNA methylation profiling and tandem repeat genotyping, we identified 24 methylated TREs and investigated their effects on human traits using PheWAS in 168,641 individuals from the UK Biobank, identifying 156 significant TRE:trait associations involving 17 different TREs. Of these, a GCC expansion in the promoter of AFF3 was linked with a 2.4-fold reduced probability of completing secondary education, an effect size comparable to several recurrent pathogenic microdeletions. In a cohort of 6,371 probands with neurodevelopmental problems of suspected genetic etiology, we observed a significant enrichment of AFF3 expansions compared to controls. With a population prevalence that is at least 5-fold higher than the TRE that causes fragile X syndrome, AFF3 expansions represent a significant cause of neurodevelopmental delay.
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11
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LaFlamme CW, Rastin C, Sengupta S, Pennington HE, Russ-Hall SJ, Schneider AL, Bonkowski ES, Almanza Fuerte EP, Galey M, Goffena J, Gibson SB, Allan TJ, Nyaga DM, Lieffering N, Hebbar M, Walker EV, Darnell D, Olsen SR, Kolekar P, Djekidel N, Rosikiewicz W, McConkey H, Kerkhof J, Levy MA, Relator R, Lev D, Lerman-Sagie T, Park KL, Alders M, Cappuccio G, Chatron N, Demain L, Genevieve D, Lesca G, Roscioli T, Sanlaville D, Tedder ML, Hubshman MW, Ketkar S, Dai H, Worley KC, Rosenfeld JA, Chao HT, Neale G, Carvill GL, Wang Z, Berkovic SF, Sadleir LG, Miller DE, Scheffer IE, Sadikovic B, Mefford HC. Diagnostic Utility of Genome-wide DNA Methylation Analysis in Genetically Unsolved Developmental and Epileptic Encephalopathies and Refinement of a CHD2 Episignature. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.11.23296741. [PMID: 37873138 PMCID: PMC10592992 DOI: 10.1101/2023.10.11.23296741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Sequence-based genetic testing currently identifies causative genetic variants in ∼50% of individuals with developmental and epileptic encephalopathies (DEEs). Aberrant changes in DNA methylation are implicated in various neurodevelopmental disorders but remain unstudied in DEEs. Rare epigenetic variations ("epivariants") can drive disease by modulating gene expression at single loci, whereas genome-wide DNA methylation changes can result in distinct "episignature" biomarkers for monogenic disorders in a growing number of rare diseases. Here, we interrogate the diagnostic utility of genome-wide DNA methylation array analysis on peripheral blood samples from 516 individuals with genetically unsolved DEEs who had previously undergone extensive genetic testing. We identified rare differentially methylated regions (DMRs) and explanatory episignatures to discover causative and candidate genetic etiologies in 10 individuals. We then used long-read sequencing to identify DNA variants underlying rare DMRs, including one balanced translocation, three CG-rich repeat expansions, and two copy number variants. We also identify pathogenic sequence variants associated with episignatures; some had been missed by previous exome sequencing. Although most DEE genes lack known episignatures, the increase in diagnostic yield for DNA methylation analysis in DEEs is comparable to the added yield of genome sequencing. Finally, we refine an episignature for CHD2 using an 850K methylation array which was further refined at higher CpG resolution using bisulfite sequencing to investigate potential insights into CHD2 pathophysiology. Our study demonstrates the diagnostic yield of genome-wide DNA methylation analysis to identify causal and candidate genetic causes as ∼2% (10/516) for unsolved DEE cases.
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12
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Mastrorosa FK, Miller DE, Eichler EE. Applications of long-read sequencing to Mendelian genetics. Genome Med 2023; 15:42. [PMID: 37316925 DOI: 10.1186/s13073-023-01194-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 05/18/2023] [Indexed: 06/16/2023] Open
Abstract
Advances in clinical genetic testing, including the introduction of exome sequencing, have uncovered the molecular etiology for many rare and previously unsolved genetic disorders, yet more than half of individuals with a suspected genetic disorder remain unsolved after complete clinical evaluation. A precise genetic diagnosis may guide clinical treatment plans, allow families to make informed care decisions, and permit individuals to participate in N-of-1 trials; thus, there is high interest in developing new tools and techniques to increase the solve rate. Long-read sequencing (LRS) is a promising technology for both increasing the solve rate and decreasing the amount of time required to make a precise genetic diagnosis. Here, we summarize current LRS technologies, give examples of how they have been used to evaluate complex genetic variation and identify missing variants, and discuss future clinical applications of LRS. As costs continue to decrease, LRS will find additional utility in the clinical space fundamentally changing how pathological variants are discovered and eventually acting as a single-data source that can be interrogated multiple times for clinical service.
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Affiliation(s)
| | - Danny E Miller
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children's Hospital, Seattle, WA, 98195, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
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13
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Chang YT, Hong SY, Lin WD, Lin CH, Lin SS, Tsai FJ, Chou IC. Genetic Testing in Children with Developmental and Epileptic Encephalopathies: A Review of Advances in Epilepsy Genomics. CHILDREN 2023; 10:children10030556. [PMID: 36980114 PMCID: PMC10047509 DOI: 10.3390/children10030556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023]
Abstract
Advances in disease-related gene discovery have led to tremendous innovations in the field of epilepsy genetics. Identification of genetic mutations that cause epileptic encephalopathies has opened new avenues for the development of targeted therapies. Clinical testing using extensive gene panels, exomes, and genomes is currently accessible and has resulted in higher rates of diagnosis and better comprehension of the disease mechanisms underlying the condition. Children with developmental disabilities have a higher risk of developing epilepsy. As our understanding of the mechanisms underlying encephalopathies and epilepsies improves, there may be greater potential to develop innovative therapies tailored to an individual’s genotype. This article provides an overview of the significant progress in epilepsy genomics in recent years, with a focus on developmental and epileptic encephalopathies in children. The aim of this review is to enhance comprehension of the clinical utilization of genetic testing in this particular patient population. The development of effective and precise therapeutic strategies for epileptic encephalopathies may be facilitated by a comprehensive understanding of their molecular pathogenesis.
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Affiliation(s)
- Yu-Tzu Chang
- School of Post Baccalaureate Chinese Medicine, China Medical University, Taichung 40447, Taiwan; (Y.-T.C.)
- Division of Pediatric Neurology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
| | - Syuan-Yu Hong
- Division of Pediatric Neurology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
- Department of Medicine, School of Medicine, China Medical University, Taichung 40447, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40447, Taiwan
| | - Wei-De Lin
- School of Post Baccalaureate Chinese Medicine, China Medical University, Taichung 40447, Taiwan; (Y.-T.C.)
- Department of Medical Research, China Medical University Hospital, Taichung 40447, Taiwan
| | - Chien-Heng Lin
- Division of Pediatric Pulmonology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
- Department of Biomedical Imaging and Radiological Science, College of Medicine, China Medial University, Taichung 40447, Taiwan
| | - Sheng-Shing Lin
- School of Post Baccalaureate Chinese Medicine, China Medical University, Taichung 40447, Taiwan; (Y.-T.C.)
- Division of Pediatric Neurology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
| | - Fuu-Jen Tsai
- Department of Medical Research, China Medical University Hospital, Taichung 40447, Taiwan
- Division of Genetics and Metabolism, China Medical University Children’s Hospital, Taichung 40447, Taiwan
- Department of Medical Genetics, China Medical University Hospital, Taichung 40447, Taiwan
- School of Chinese Medicine, China Medical University, Taichung 40447, Taiwan
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 40447, Taiwan
| | - I-Ching Chou
- Division of Pediatric Neurology, China Medical University Children’s Hospital, Taichung 40447, Taiwan
- Graduate Institute of Integrated Medicine, China Medical University, Taichung 40447, Taiwan
- Correspondence: ; Tel.: +886-4-22052121
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14
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Hamanaka K, Yamauchi D, Koshimizu E, Watase K, Mogushi K, Ishikawa K, Mizusawa H, Tsuchida N, Uchiyama Y, Fujita A, Misawa K, Mizuguchi T, Miyatake S, Matsumoto N. Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans. Genome Res 2023; 33:435-447. [PMID: 37307504 PMCID: PMC10078293 DOI: 10.1101/gr.277335.122] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 02/22/2023] [Indexed: 03/29/2023]
Abstract
Tandem repeats (TRs) are one of the largest sources of polymorphism, and their length is associated with gene regulation. Although previous studies reported several tandem repeats regulating gene splicing in cis (spl-TRs), no large-scale study has been conducted. In this study, we established a genome-wide catalog of 9537 spl-TRs with a total of 58,290 significant TR-splicing associations across 49 tissues (false discovery rate 5%) by using Genotype-Tissue expression (GTex) Project data. Regression models explaining splicing variation by using spl-TRs and other flanking variants suggest that at least some of the spl-TRs directly modulate splicing. In our catalog, two spl-TRs are known loci for repeat expansion diseases, spinocerebellar ataxia 6 (SCA6) and 12 (SCA12). Splicing alterations by these spl-TRs were compatible with those observed in SCA6 and SCA12. Thus, our comprehensive spl-TR catalog may help elucidate the pathomechanism of genetic diseases.
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Affiliation(s)
- Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | | | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Kei Watase
- Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Kaoru Mogushi
- Intractable Disease Research Center, Juntendo University Graduate School of Medicine, Tokyo 113-8421, Japan
| | - Kinya Ishikawa
- The Center for Personalized Medicine for Healthy Aging, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Hidehiro Mizusawa
- Department of Neurology, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8551, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Kazuharu Misawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan
- Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Kanagawa 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa 236-0004, Japan;
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15
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Ronco R, Perini C, Currò R, Dominik N, Facchini S, Gennari A, Simone R, Stuart S, Nagy S, Vegezzi E, Quartesan I, El-Saddig A, Lavin T, Tucci A, Szymura A, Novis De Farias LE, Gary A, Delfeld M, Kandikatla P, Niu N, Tawde S, Shaw J, Polke J, Reilly MM, Wood NW, Crespan E, Gomez C, Chen JYH, Schmahmann JD, Gosal D, Houlden H, Das S, Cortese A. Truncating Variants in RFC1 in Cerebellar Ataxia, Neuropathy, and Vestibular Areflexia Syndrome. Neurology 2023; 100:e543-e554. [PMID: 36289003 PMCID: PMC9931080 DOI: 10.1212/wnl.0000000000201486] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/14/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND AND OBJECTIVE Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS) is an autosomal recessive neurodegenerative disease characterized by adult-onset and slowly progressive sensory neuropathy, cerebellar dysfunction, and vestibular impairment. In most cases, the disease is caused by biallelic (AAGGG)n repeat expansions in the second intron of the replication factor complex subunit 1 (RFC1). However, a small number of cases with typical CANVAS do not carry the common biallelic repeat expansion. The objective of this study was to expand the genotypic spectrum of CANVAS by identifying sequence variants in RFC1-coding region associated with this condition. METHODS Fifteen individuals diagnosed with CANVAS and carrying only 1 heterozygous (AAGGG)n expansion in RFC1 underwent whole-genome sequencing or whole-exome sequencing to test for the presence of a second variant in RFC1 or other unrelated gene. To assess the effect of truncating variants on RFC1 expression, we tested the level of RFC1 transcript and protein on patients' derived cell lines. RESULTS We identified 7 patients from 5 unrelated families with clinically defined CANVAS carrying a heterozygous (AAGGG)n expansion together with a second truncating variant in trans in RFC1, which included the following: c.1267C>T (p.Arg423Ter), c.1739_1740del (p.Lys580SerfsTer9), c.2191del (p.Gly731GlufsTer6), and c.2876del (p.Pro959GlnfsTer24). Patient fibroblasts containing the c.1267C>T (p.Arg423Ter) or c.2876del (p.Pro959GlnfsTer24) variants demonstrated nonsense-mediated mRNA decay and reduced RFC1 transcript and protein. DISCUSSION Our report expands the genotype spectrum of RFC1 disease. Full RFC1 sequencing is recommended in cases affected by typical CANVAS and carrying monoallelic (AAGGG)n expansions. In addition, it sheds further light on the pathogenesis of RFC1 CANVAS because it supports the existence of a loss-of-function mechanism underlying this complex neurodegenerative condition.
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Affiliation(s)
- Riccardo Ronco
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Cecilia Perini
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Riccardo Currò
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Natalia Dominik
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Stefano Facchini
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Alice Gennari
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Roberto Simone
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Skye Stuart
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Sara Nagy
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Elisa Vegezzi
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Ilaria Quartesan
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Amar El-Saddig
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Timothy Lavin
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Arianna Tucci
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Agnieszka Szymura
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Luiz Eduardo Novis De Farias
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Alexander Gary
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Megan Delfeld
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Priscilla Kandikatla
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Nifang Niu
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Sanjukta Tawde
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Joseph Shaw
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - James Polke
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Mary M Reilly
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Nick W Wood
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Emmanuele Crespan
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Christopher Gomez
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Jin Yun Helen Chen
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Jeremy Dan Schmahmann
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - David Gosal
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Henry Houlden
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Soma Das
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Andrea Cortese
- From the Department of Neuromuscular Diseases (R.R., R.C., N.D., S.F., Alice Gennari, R.S., S.S., S.N., A.T., A.S., L.E.N.D.F., M.M.R., N.W.W., H.H., A.C.), UCL Queen Square Institute of Neurology, London, United Kingdom; Department of Brain and Behavioral Sciences (R.R., R.C., I.Q., A.C.), University of Pavia, Pavia, Italy; Institute of Molecular Genetics IGM-CNR "Luigi Luca Cavalli-Sforza" (C.P., E.C.), Italy; Department of Neurology (S.N.), University Hospital Basel, University of Basel, Switzerland; IRCCS Mondino Foundation (E.V.), Pavia, Italy; Manchester Centre for Clinical Neurosciences (A.E.-S., T.L., D.G.), Salford Royal Hospital, Northern Care Alliance NHS Foundation Trust, Manchester, United Kingdom; Clinical Pharmacology (A.T.), William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, United Kingdom; Departamento de Distúrbios do Movimento (L.E.N.D.F.), Hospital Das Clínicas Da Universidade Federal Do Paraná, Curitiba, Brazil; University of Chicago Medical Center (Alexander Gary, M.D., P.K., S.D.), The University of Chicago, IL; Department of Human Genetics (N.N., S.T.), The University of Chicago, IL; Neurogenetics (J.S., J.P.), University College London Hospitals NHS Foundation Trust, National Hospital for Neurology and Neurosurgery, London, United Kingdom; Department of Neurology (C.G.), The University of Chicago, IL; and Ataxia Center (J.Y.H.C., J.D.S.), Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston.
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16
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The Power of Clinical Diagnosis for Deciphering Complex Genetic Mechanisms in Rare Diseases. Genes (Basel) 2023; 14:genes14010196. [PMID: 36672937 PMCID: PMC9858967 DOI: 10.3390/genes14010196] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Complex genetic disease mechanisms, such as structural or non-coding variants, currently pose a substantial difficulty in frontline diagnostic tests. They thus may account for most unsolved rare disease patients regardless of the clinical phenotype. However, the clinical diagnosis can narrow the genetic focus to just a couple of genes for patients with well-established syndromes defined by prominent physical and/or unique biochemical phenotypes, allowing deeper analyses to consider complex genetic origin. Then, clinical-diagnosis-driven genome sequencing strategies may expedite the development of testing and analytical methods to account for complex disease mechanisms as well as to advance functional assays for the confirmation of complex variants, clinical management, and the development of new therapies.
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17
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Nabariya DK, Heinz A, Derksen S, Krauß S. Intracellular and intercellular transport of RNA organelles in CXG repeat disorders: The strength of weak ties. Front Mol Biosci 2022; 9:1000932. [PMID: 36589236 PMCID: PMC9800848 DOI: 10.3389/fmolb.2022.1000932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
RNA is a vital biomolecule, the function of which is tightly spatiotemporally regulated. RNA organelles are biological structures that either membrane-less or surrounded by membrane. They are produced by the all the cells and indulge in vital cellular mechanisms. They include the intracellular RNA granules and the extracellular exosomes. RNA granules play an essential role in intracellular regulation of RNA localization, stability and translation. Aberrant regulation of RNA is connected to disease development. For example, in microsatellite diseases such as CXG repeat expansion disorders, the mutant CXG repeat RNA's localization and function are affected. RNA is not only transported intracellularly but can also be transported between cells via exosomes. The loading of the exosomes is regulated by RNA-protein complexes, and recent studies show that cytosolic RNA granules and exosomes share common content. Intracellular RNA granules and exosome loading may therefore be related. Exosomes can also transfer pathogenic molecules of CXG diseases from cell to cell, thereby driving disease progression. Both intracellular RNA granules and extracellular RNA vesicles may serve as a source for diagnostic and treatment strategies. In therapeutic approaches, pharmaceutical agents may be loaded into exosomes which then transport them to the desired cells/tissues. This is a promising target specific treatment strategy with few side effects. With respect to diagnostics, disease-specific content of exosomes, e.g., RNA-signatures, can serve as attractive biomarker of central nervous system diseases detecting early physiological disturbances, even before symptoms of neurodegeneration appear and irreparable damage to the nervous system occurs. In this review, we summarize the known function of cytoplasmic RNA granules and extracellular vesicles, as well as their role and dysfunction in CXG repeat expansion disorders. We also provide a summary of established protocols for the isolation and characterization of both cytoplasmic and extracellular RNA organelles.
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Affiliation(s)
| | | | | | - Sybille Krauß
- Human Biology/Neurobiology, Institute of Biology, Faculty IV, School of Science and Technology, University of Siegen, Siegen, Germany
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18
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Dashnow H, Pedersen BS, Hiatt L, Brown J, Beecroft SJ, Ravenscroft G, LaCroix AJ, Lamont P, Roxburgh RH, Rodrigues MJ, Davis M, Mefford HC, Laing NG, Quinlan AR. STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci. Genome Biol 2022; 23:257. [PMID: 36517892 PMCID: PMC9753380 DOI: 10.1186/s13059-022-02826-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
Expansions of short tandem repeats (STRs) cause many rare diseases. Expansion detection is challenging with short-read DNA sequencing data since supporting reads are often mapped incorrectly. Detection is particularly difficult for "novel" STRs, which include new motifs at known loci or STRs absent from the reference genome. We developed STRling to efficiently count k-mers to recover informative reads and call expansions at known and novel STR loci. STRling is sensitive to known STR disease loci, has a low false discovery rate, and resolves novel STR expansions to base-pair position accuracy. It is fast, scalable, open-source, and available at: github.com/quinlan-lab/STRling .
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Affiliation(s)
- Harriet Dashnow
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah, Salt Lake City, UT USA
| | - Brent S. Pedersen
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah, Salt Lake City, UT USA ,grid.7692.a0000000090126352Utrecht University Medical Center, Utrecht, The Netherlands
| | - Laurel Hiatt
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah, Salt Lake City, UT USA
| | - Joe Brown
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah, Salt Lake City, UT USA
| | - Sarah J. Beecroft
- Pawsey Supercomputing Research Centre, Kensington, WA Australia ,grid.1012.20000 0004 1936 7910Harry Perkins Institute of Medical Research and Centre for Medical Research, University of Western Australia, Perth, WA Australia
| | - Gianina Ravenscroft
- grid.1012.20000 0004 1936 7910Harry Perkins Institute of Medical Research and Centre for Medical Research, University of Western Australia, Perth, WA Australia
| | - Amy J. LaCroix
- grid.34477.330000000122986657Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195 USA
| | - Phillipa Lamont
- grid.416195.e0000 0004 0453 3875Neurogenetic Unit, Royal Perth Hospital, Perth, WA Australia
| | - Richard H. Roxburgh
- grid.414055.10000 0000 9027 2851Neurology, Auckland City Hospital, Auckland, New Zealand
| | - Miriam J. Rodrigues
- grid.414055.10000 0000 9027 2851Neurology, Auckland City Hospital, Auckland, New Zealand ,grid.9654.e0000 0004 0372 3343Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Mark Davis
- grid.413880.60000 0004 0453 2856Neurogenetics Unit, Department of Diagnostic Genomics, PathWest Laboratory Medicine, Western Australian Department of Health, Nedlands, Australia
| | - Heather C. Mefford
- grid.34477.330000000122986657Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195 USA
| | - Nigel G. Laing
- grid.1012.20000 0004 1936 7910Harry Perkins Institute of Medical Research and Centre for Medical Research, University of Western Australia, Perth, WA Australia ,grid.413880.60000 0004 0453 2856Neurogenetics Unit, Department of Diagnostic Genomics, PathWest Laboratory Medicine, Western Australian Department of Health, Nedlands, Australia
| | - Aaron R. Quinlan
- grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah, Salt Lake City, UT USA
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19
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Mirceta M, Shum N, Schmidt MHM, Pearson CE. Fragile sites, chromosomal lesions, tandem repeats, and disease. Front Genet 2022; 13:985975. [PMID: 36468036 PMCID: PMC9714581 DOI: 10.3389/fgene.2022.985975] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/02/2022] [Indexed: 09/16/2023] Open
Abstract
Expanded tandem repeat DNAs are associated with various unusual chromosomal lesions, despiralizations, multi-branched inter-chromosomal associations, and fragile sites. Fragile sites cytogenetically manifest as localized gaps or discontinuities in chromosome structure and are an important genetic, biological, and health-related phenomena. Common fragile sites (∼230), present in most individuals, are induced by aphidicolin and can be associated with cancer; of the 27 molecularly-mapped common sites, none are associated with a particular DNA sequence motif. Rare fragile sites ( ≳ 40 known), ≤ 5% of the population (may be as few as a single individual), can be associated with neurodevelopmental disease. All 10 molecularly-mapped folate-sensitive fragile sites, the largest category of rare fragile sites, are caused by gene-specific CGG/CCG tandem repeat expansions that are aberrantly CpG methylated and include FRAXA, FRAXE, FRAXF, FRA2A, FRA7A, FRA10A, FRA11A, FRA11B, FRA12A, and FRA16A. The minisatellite-associated rare fragile sites, FRA10B, FRA16B, can be induced by AT-rich DNA-ligands or nucleotide analogs. Despiralized lesions and multi-branched inter-chromosomal associations at the heterochromatic satellite repeats of chromosomes 1, 9, 16 are inducible by de-methylating agents like 5-azadeoxycytidine and can spontaneously arise in patients with ICF syndrome (Immunodeficiency Centromeric instability and Facial anomalies) with mutations in genes regulating DNA methylation. ICF individuals have hypomethylated satellites I-III, alpha-satellites, and subtelomeric repeats. Ribosomal repeats and subtelomeric D4Z4 megasatellites/macrosatellites, are associated with chromosome location, fragility, and disease. Telomere repeats can also assume fragile sites. Dietary deficiencies of folate or vitamin B12, or drug insults are associated with megaloblastic and/or pernicious anemia, that display chromosomes with fragile sites. The recent discovery of many new tandem repeat expansion loci, with varied repeat motifs, where motif lengths can range from mono-nucleotides to megabase units, could be the molecular cause of new fragile sites, or other chromosomal lesions. This review focuses on repeat-associated fragility, covering their induction, cytogenetics, epigenetics, cell type specificity, genetic instability (repeat instability, micronuclei, deletions/rearrangements, and sister chromatid exchange), unusual heritability, disease association, and penetrance. Understanding tandem repeat-associated chromosomal fragile sites provides insight to chromosome structure, genome packaging, genetic instability, and disease.
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Affiliation(s)
- Mila Mirceta
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Natalie Shum
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Monika H. M. Schmidt
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Christopher E. Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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Kurosaki T, Ashizawa T. The genetic and molecular features of the intronic pentanucleotide repeat expansion in spinocerebellar ataxia type 10. Front Genet 2022; 13:936869. [PMID: 36199580 PMCID: PMC9528567 DOI: 10.3389/fgene.2022.936869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
Spinocerebellar ataxia type 10 (SCA10) is characterized by progressive cerebellar neurodegeneration and, in many patients, epilepsy. This disease mainly occurs in individuals with Indigenous American or East Asian ancestry, with strong evidence supporting a founder effect. The mutation causing SCA10 is a large expansion in an ATTCT pentanucleotide repeat in intron 9 of the ATXN10 gene. The ATTCT repeat is highly unstable, expanding to 280–4,500 repeats in affected patients compared with the 9–32 repeats in normal individuals, one of the largest repeat expansions causing neurological disorders identified to date. However, the underlying molecular basis of how this huge repeat expansion evolves and contributes to the SCA10 phenotype remains largely unknown. Recent progress in next-generation DNA sequencing technologies has established that the SCA10 repeat sequence has a highly heterogeneous structure. Here we summarize what is known about the structure and origin of SCA10 repeats, discuss the potential contribution of variant repeats to the SCA10 disease phenotype, and explore how this information can be exploited for therapeutic benefit.
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Affiliation(s)
- Tatsuaki Kurosaki
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY, United States
- Center for RNA Biology, University of Rochester, Rochester, NY, United States
- *Correspondence: Tatsuaki Kurosaki, ; Tetsuo Ashizawa,
| | - Tetsuo Ashizawa
- Stanley H. Appel Department of Neurology, Houston Methodist Research Institute and Weil Cornell Medical College at Houston Methodist Houston, TX, United States
- *Correspondence: Tatsuaki Kurosaki, ; Tetsuo Ashizawa,
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21
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Yousuf A, Ahmed N, Qurashi A. Non-canonical DNA/RNA structures associated with the pathogenesis of Fragile X-associated tremor/ataxia syndrome and Fragile X syndrome. Front Genet 2022; 13:866021. [PMID: 36110216 PMCID: PMC9468596 DOI: 10.3389/fgene.2022.866021] [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: 01/30/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
Fragile X-associated tremor/ataxia syndrome (FXTAS) and fragile X syndrome (FXS) are primary examples of fragile X-related disorders (FXDs) caused by abnormal expansion of CGG repeats above a certain threshold in the 5'-untranslated region of the fragile X mental retardation (FMR1) gene. Both diseases have distinct clinical manifestations and molecular pathogenesis. FXTAS is a late-adult-onset neurodegenerative disorder caused by a premutation (PM) allele (CGG expansion of 55-200 repeats), resulting in FMR1 gene hyperexpression. On the other hand, FXS is a neurodevelopmental disorder that results from a full mutation (FM) allele (CGG expansions of ≥200 repeats) leading to heterochromatization and transcriptional silencing of the FMR1 gene. The main challenge is to determine how CGG repeat expansion affects the fundamentally distinct nature of FMR1 expression in FM and PM ranges. Abnormal CGG repeat expansions form a variety of non-canonical DNA and RNA structures that can disrupt various cellular processes and cause distinct effects in PM and FM alleles. Here, we review these structures and how they are related to underlying mutations and disease pathology in FXS and FXTAS. Finally, as new CGG expansions within the genome have been identified, it will be interesting to determine their implications in disease pathology and treatment.
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Affiliation(s)
| | | | - Abrar Qurashi
- Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
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22
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Halman A, Dolzhenko E, Oshlack A. STRipy: A graphical application for enhanced genotyping of pathogenic short tandem repeats in sequencing data. Hum Mutat 2022; 43:859-868. [PMID: 35395114 PMCID: PMC9541159 DOI: 10.1002/humu.24382] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/01/2021] [Accepted: 04/06/2022] [Indexed: 11/22/2022]
Abstract
Expansions of short tandem repeats (STRs) have been implicated as the causal variant in over 50 diseases known to date. There are several tools which can genotype STRs from high-throughput sequencing (HTS) data. However, running these tools out of the box only allows around half of the known disease-causing loci to be genotyped. Furthermore, the genotypes estimated at these loci are often underestimated with maximum lengths limited to either the read or fragment length, which is less than the pathogenic cutoff for some diseases. Although analysis tools can be customized to genotype extra loci, this requires proficiency in bioinformatics to set up, limiting their widespread usage by other researchers and clinicians. To address these issues, we have developed a new software called STRipy, which is able to target all known disease-causing STRs from HTS data. We created an intuitive graphical interface for STRipy and significantly simplified the detection of STRs expansions. Moreover, we genotyped all disease loci for over two and half thousand samples to provide population-wide distributions to assist with interpretation of results. We believe the simplicity and breadth of STRipy will increase the genotyping of STRs in sequencing data resulting in further diagnoses of rare STR diseases.
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Affiliation(s)
- Andreas Halman
- Peter MacCallum Cancer CentreMelbourneVictoriaAustralia
- Sir Peter MacCallum Department of OncologyThe University of MelbourneParkvilleVictoriaAustralia
- Murdoch Children's Research Institute, Royal Children's HospitalParkvilleVictoriaAustralia
- Florey Department of Neuroscience and Mental HealthThe University of MelbourneParkvilleVictoriaAustralia
- School of Natural Sciences and HealthTallinn UniversityTallinnEstonia
| | | | - Alicia Oshlack
- Peter MacCallum Cancer CentreMelbourneVictoriaAustralia
- Sir Peter MacCallum Department of OncologyThe University of MelbourneParkvilleVictoriaAustralia
- School of BioSciencesUniversity of MelbourneParkvilleVictoriaAustralia
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Shen F, Yang Y, Zheng Y, Tu M, Zhao L, Luo Z, Fu Y, Zhu Y. Mutant B3GALT6 in a Multiplex Family: A Dominant Variant Co-Segregated With Moderate Malformations. Front Genet 2022; 13:824445. [PMID: 35734427 PMCID: PMC9207203 DOI: 10.3389/fgene.2022.824445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/25/2022] [Indexed: 11/25/2022] Open
Abstract
B3GALT6 is a well-documented disease-related gene. Several B3GALT6-recessive variants have been reported to cause Ehlers–Danlos syndrome (EDS). To the best of our knowledge, no dominant B3GALT6 variant that causes human disease has been reported. In 2012, we reported on a three-generation, autosomal-dominant family with multiple members who suffered from radioulnar joint rotation limitation, scoliosis, thick vermilion of both lips, and others, but the genetic cause was unknown. Here, exome sequencing of the family identified mutant B3GALT6 as the cause of the multiplex affected family. We observed that, in the compound heterozygous pattern (i.e., c.883C>T:p.R295C and c.510_517del:p.L170fs*268), mutant B3GALT6 led to severe consequences, and in the dominant pattern, an elongated B3GALT6 variant co-segregated with moderate phenotypes. The functional experiments were performed in vitro. The R295C variant led to subcellular mislocalization, whereas the L170fs*268 showed normal subcellular localization, but it led to an elongated protein. Given that most of the catalytic galactosyltransferase domain was disrupted for the L170fs*268 (it is unlikely that such a protein has activity), we propose that the L170fs*268 occupies the normal B3GALT6 protein position in the Golgi and exerts a dominant-negative effect.
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Affiliation(s)
- Fang Shen
- The Laboratory of Genetics and Metabolism, Pediatrics Research Institute of Hunan Province, Hunan Children’s Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Yongjia Yang
- The Laboratory of Genetics and Metabolism, Pediatrics Research Institute of Hunan Province, Hunan Children’s Hospital, Hengyang Medical School, University of South China, Changsha, China
- *Correspondence: Yongjia Yang, ; Yimin Zhu,
| | - Yu Zheng
- The Laboratory of Genetics and Metabolism, Pediatrics Research Institute of Hunan Province, Hunan Children’s Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Ming Tu
- The Laboratory of Genetics and Metabolism, Pediatrics Research Institute of Hunan Province, Hunan Children’s Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Liu Zhao
- The Laboratory of Genetics and Metabolism, Pediatrics Research Institute of Hunan Province, Hunan Children’s Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Zhenqing Luo
- The Laboratory of Genetics and Metabolism, Pediatrics Research Institute of Hunan Province, Hunan Children’s Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Yuyan Fu
- The Laboratory of Genetics and Metabolism, Pediatrics Research Institute of Hunan Province, Hunan Children’s Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Yimin Zhu
- The Laboratory of Genetics and Metabolism, Pediatrics Research Institute of Hunan Province, Hunan Children’s Hospital, Hengyang Medical School, University of South China, Changsha, China
- Emergency Research Institute of Hunan Province, Hunan People’s Hospital, Changsha, China
- *Correspondence: Yongjia Yang, ; Yimin Zhu,
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24
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Boldyreva LV, Andreyeva EN, Pindyurin AV. Position Effect Variegation: Role of the Local Chromatin Context in Gene Expression Regulation. Mol Biol 2022. [DOI: 10.1134/s0026893322030049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Fakharzadeh A, Zhang J, Roland C, Sagui C. Novel eGZ-motif formed by regularly extruded guanine bases in a left-handed Z-DNA helix as a major motif behind CGG trinucleotide repeats. Nucleic Acids Res 2022; 50:4860-4876. [PMID: 35536254 PMCID: PMC9122592 DOI: 10.1093/nar/gkac339] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/19/2022] [Accepted: 05/05/2022] [Indexed: 12/19/2022] Open
Abstract
The expansion of d(CGG) trinucleotide repeats (TRs) lies behind several important neurodegenerative diseases. Atypical DNA secondary structures have been shown to trigger TR expansion: their characterization is important for a molecular understanding of TR disease. CD spectroscopy experiments in the last decade have unequivocally demonstrated that CGG runs adopt a left-handed Z-DNA conformation, whose features remain uncertain because it entails accommodating GG mismatches. In order to find this missing motif, we have carried out molecular dynamics (MD) simulations to explore all the possible Z-DNA helices that potentially form after the transition from B- to Z-DNA. Such helices combine either CpG or GpC Watson-Crick steps in Z-DNA form with GG-mismatch conformations set as either intrahelical or extrahelical; and participating in BZ or ZZ junctions or in alternately extruded conformations. Characterization of the stability and structural features (especially overall left-handedness, higher-temperature and steered MD simulations) identified two novel Z-DNA helices: the most stable one displays alternately extruded Gs, and is followed by a helix with symmetrically extruded ZZ junctions. The G-extrusion favors a seamless stacking of the Watson-Crick base pairs; extruded Gs favor syn conformations and display hydrogen-bonding and stacking interactions. Such conformations could have the potential to hijack the MMR complex, thus triggering further expansion.
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Affiliation(s)
- Ashkan Fakharzadeh
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Jiahui Zhang
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Christopher Roland
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
| | - Celeste Sagui
- Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA
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26
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Freeze HH, Jaeken J, Matthijs G. CDG or not CDG. J Inherit Metab Dis 2022; 45:383-385. [PMID: 35338706 PMCID: PMC9121739 DOI: 10.1002/jimd.12498] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/16/2022] [Accepted: 03/24/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Hudson H. Freeze
- Human Genetics Program, Sanford Burnham Prebys, La Jolla, CA 92037, USA
| | - Jaak Jaeken
- Center of Metabolic Diseases, KU Leuven, Leuven, Belgium
| | - Gert Matthijs
- Department of Human Genetics, KU Leuven, Leuven, Belgium
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27
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Schwartz NB, Domowicz MS. Roles of Chondroitin Sulfate Proteoglycans as Regulators of Skeletal Development. Front Cell Dev Biol 2022; 10:745372. [PMID: 35465334 PMCID: PMC9026158 DOI: 10.3389/fcell.2022.745372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 03/21/2022] [Indexed: 11/29/2022] Open
Abstract
The extracellular matrix (ECM) is critically important for most cellular processes including differentiation, morphogenesis, growth, survival and regeneration. The interplay between cells and the ECM often involves bidirectional signaling between ECM components and small molecules, i.e., growth factors, morphogens, hormones, etc., that regulate critical life processes. The ECM provides biochemical and contextual information by binding, storing, and releasing the bioactive signaling molecules, and/or mechanical information that signals from the cell membrane integrins through the cytoskeleton to the nucleus, thereby influencing cell phenotypes. Using these dynamic, reciprocal processes, cells can also remodel and reshape the ECM by degrading and re-assembling it, thereby sculpting their environments. In this review, we summarize the role of chondroitin sulfate proteoglycans as regulators of cell and tissue development using the skeletal growth plate model, with an emphasis on use of naturally occurring, or created mutants to decipher the role of proteoglycan components in signaling paradigms.
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Affiliation(s)
- Nancy B. Schwartz
- Department of Pediatrics, Biological Sciences Division, The University of Chicago, Chicago, IL, United States
- Department of Biochemistry and Molecular Biology, Biological Sciences Division, The University of Chicago, Chicago, IL, United States
- *Correspondence: Nancy B. Schwartz,
| | - Miriam S. Domowicz
- Department of Pediatrics, Biological Sciences Division, The University of Chicago, Chicago, IL, United States
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28
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Baxter SM, Posey JE, Lake NJ, Sobreira N, Chong JX, Buyske S, Blue EE, Chadwick LH, Coban-Akdemir ZH, Doheny KF, Davis CP, Lek M, Wellington C, Jhangiani SN, Gerstein M, Gibbs RA, Lifton RP, MacArthur DG, Matise TC, Lupski JR, Valle D, Bamshad MJ, Hamosh A, Mane S, Nickerson DA, Rehm HL, O'Donnell-Luria A. Centers for Mendelian Genomics: A decade of facilitating gene discovery. Genet Med 2022; 24:784-797. [PMID: 35148959 PMCID: PMC9119004 DOI: 10.1016/j.gim.2021.12.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/08/2021] [Accepted: 12/12/2021] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Mendelian disease genomic research has undergone a massive transformation over the past decade. With increasing availability of exome and genome sequencing, the role of Mendelian research has expanded beyond data collection, sequencing, and analysis to worldwide data sharing and collaboration. METHODS Over the past 10 years, the National Institutes of Health-supported Centers for Mendelian Genomics (CMGs) have played a major role in this research and clinical evolution. RESULTS We highlight the cumulative gene discoveries facilitated by the program, biomedical research leveraged by the approach, and the larger impact on the research community. Beyond generating a list of gene-phenotype relationships and participating in widespread data sharing, the CMGs have created resources, tools, and training for the larger community to foster understanding of genes and genome variation. The CMGs have participated in a wide range of data sharing activities, including deposition of all eligible CMG data into the Analysis, Visualization, and Informatics Lab-space (AnVIL), sharing candidate genes through the Matchmaker Exchange and the CMG website, and sharing variants in Genotypes to Mendelian Phenotypes (Geno2MP) and VariantMatcher. CONCLUSION The work is far from complete; strengthening communication between research and clinical realms, continued development and sharing of knowledge and tools, and improving access to richly characterized data sets are all required to diagnose the remaining molecularly undiagnosed patients.
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Affiliation(s)
- Samantha M Baxter
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA.
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Nicole J Lake
- Department of Genetics, Yale School of Medicine, New Haven, CT; Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Nara Sobreira
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Jessica X Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA; Brotman Baty Institute for Precision Medicine, Seattle, WA
| | - Steven Buyske
- Department of Statistics, Rutgers University, Piscataway, NJ; Department of Genetics, Rutgers University, Piscataway, NJ
| | - Elizabeth E Blue
- Brotman Baty Institute for Precision Medicine, Seattle, WA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Lisa H Chadwick
- Division of Genome Sciences, National Human Genome Research Institute, Bethesda, MD
| | - Zeynep H Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX
| | - Kimberly F Doheny
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Colleen P Davis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Genetics, Yale School of Medicine, New Haven, CT
| | | | | | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Richard P Lifton
- Department of Genetics, Yale School of Medicine, New Haven, CT; Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, New South Wales, Australia; Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Tara C Matise
- Department of Genetics, Rutgers University, Piscataway, NJ
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX; Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - David Valle
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Michael J Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA; Brotman Baty Institute for Precision Medicine, Seattle, WA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Ada Hamosh
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Shrikant Mane
- Department of Genetics, Yale School of Medicine, New Haven, CT
| | - Deborah A Nickerson
- Brotman Baty Institute for Precision Medicine, Seattle, WA; Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Heidi L Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA.
| | - Anne O'Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA; Department of Pediatrics, Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA.
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29
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Yu J, Shan J, Yu M, Di L, Xie Z, Zhang W, Lv H, Meng L, Zheng Y, Zhao Y, Gang Q, Guo X, Wang Y, Xi J, Zhu W, Da Y, Hong D, Yuan Y, Yan C, Wang Z, Deng J. The CGG repeat expansion in RILPL1 is associated with oculopharyngodistal myopathy type 4. Am J Hum Genet 2022; 109:533-541. [PMID: 35148830 DOI: 10.1016/j.ajhg.2022.01.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/20/2022] [Indexed: 12/13/2022] Open
Abstract
Recent studies indicate that CGG repeat expansions in LRP12, GIPC1, and NOTCH2NLC are associated with oculopharyngodistal myopathy (OPDM) types 1, 2, and 3, respectively. However, some clinicopathologically confirmed OPDM cases continue to have unknown genetic causes. Here, through a combination of long-read whole-genome sequencing (LRS), repeat-primed polymerase chain reaction (RP-PCR), and fluorescence amplicon length analysis PCR (AL-PCR), we found that a CGG repeat expansion in the 5' UTR of RILPL1 is associated with familial and simplex OPDM type 4 (OPDM4). The number of repeats ranged from 139 to 197. Methylation analysis indicates that the methylation levels in RILPL1 were unaltered in OPDM4 individuals. Analyses of muscle biopsies suggested that the expanded CGG repeat might be translated into a toxic poly-glycine protein that co-localizes with p62 in intranuclear inclusions. Moreover, analyses suggest that the toxic RNA gain-of-function effects also contributed to the pathogenesis of this disease. Intriguingly, all four types of OPDM have been found to be associated with the CGG repeat expansions located in 5' UTRs. This finding suggests that a common pathogenic mechanism, driven by the CGG repeat expansion, might underlie all cases of OPDM.
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30
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Boivin M, Charlet-Berguerand N. Trinucleotide CGG Repeat Diseases: An Expanding Field of Polyglycine Proteins? Front Genet 2022; 13:843014. [PMID: 35295941 PMCID: PMC8918734 DOI: 10.3389/fgene.2022.843014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 01/31/2022] [Indexed: 12/30/2022] Open
Abstract
Microsatellites are repeated DNA sequences of 3–6 nucleotides highly variable in length and sequence and that have important roles in genomes regulation and evolution. However, expansion of a subset of these microsatellites over a threshold size is responsible of more than 50 human genetic diseases. Interestingly, some of these disorders are caused by expansions of similar sequences, sizes and localizations and present striking similarities in clinical manifestations and histopathological features, which suggest a common mechanism of disease. Notably, five identical CGG repeat expansions, but located in different genes, are the causes of fragile X-associated tremor/ataxia syndrome (FXTAS), neuronal intranuclear inclusion disease (NIID), oculopharyngodistal myopathy type 1 to 3 (OPDM1-3) and oculopharyngeal myopathy with leukoencephalopathy (OPML), which are neuromuscular and neurodegenerative syndromes with overlapping symptoms and similar histopathological features, notably the presence of characteristic eosinophilic ubiquitin-positive intranuclear inclusions. In this review we summarize recent finding in neuronal intranuclear inclusion disease and FXTAS, where the causing CGG expansions were found to be embedded within small upstream ORFs (uORFs), resulting in their translation into novel proteins containing a stretch of polyglycine (polyG). Importantly, expression of these polyG proteins is toxic in animal models and is sufficient to reproduce the formation of ubiquitin-positive intranuclear inclusions. These data suggest the existence of a novel class of human genetic pathology, the polyG diseases, and question whether a similar mechanism may exist in other diseases, notably in OPDM and OPML.
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31
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Small Molecule Screening Discovers Compounds that Reduce FMRpolyG Protein Aggregates and Splicing Defect Toxicity in Fragile X-Associated Tremor/Ataxia Syndrome. Mol Neurobiol 2022; 59:1992-2007. [PMID: 35040038 DOI: 10.1007/s12035-021-02697-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 12/10/2021] [Indexed: 12/20/2022]
Abstract
Expansion of CGG trinucleotide repeats in 5' untranslated region of the FMR1 gene is the causative mutation of neurological diseases such as fragile X syndrome (FXS), fragile X-associated tremor/ataxia syndrome (FXTAS), and ovarian disorder such as fragile X-associated primary ovarian insufficiency (FXPOI). CGG repeats containing FMR1 transcripts form the toxic ribonuclear aggregates, abrupt pre-mRNA splicing, and cause repeat-associated non-AUG translation, leading to the disease symptoms. Here, we utilized a small molecule library of ~ 250,000 members obtained from the National Cancer Institute (NCI) and implemented a shape-based screening approach to identify the candidate small molecules that mitigate toxic CGG RNA-mediated pathogenesis. The compounds obtained from screening were further assessed for their affinity and selectivity towards toxic CGG repeat RNA by employing fluorescence-binding experiment and isothermal calorimetry titration assay. Three candidate molecules B1, B4, and B11 showed high affinity and selectivity for expanded CGG repeats RNA. Further, NMR spectroscopy, gel mobility shift assay, CD spectroscopy, UV-thermal denaturation assay, and molecular docking affirmed their high affinity and selectivity for toxic CGG RNAs. Next, these lead compounds selectively improved the pre-mRNA alternative splicing defects with no perturbation in global splicing efficacy and simultaneously reduced the FMR1polyG protein aggregate formation without affecting the downstream expression of the gene. Taken together these findings, we addressed compound B1, B4, and B11 as potential lead molecules for developing promising therapeutics against FXTAS. Herein, this study, we have utilized shape similarity approach to screen the NCI library and found out the potential candidate which improves the pre-mRNA splicing defects and reduces FMR1polyG aggregations.
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32
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Loureiro JR, Castro AF, Figueiredo AS, Silveira I. Molecular Mechanisms in Pentanucleotide Repeat Diseases. Cells 2022; 11:cells11020205. [PMID: 35053321 PMCID: PMC8773600 DOI: 10.3390/cells11020205] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 02/01/2023] Open
Abstract
The number of neurodegenerative diseases resulting from repeat expansion has increased extraordinarily in recent years. In several of these pathologies, the repeat can be transcribed in RNA from both DNA strands producing, at least, one toxic RNA repeat that causes neurodegeneration by a complex mechanism. Recently, seven diseases have been found caused by a novel intronic pentanucleotide repeat in distinct genes encoding proteins highly expressed in the cerebellum. These disorders are clinically heterogeneous being characterized by impaired motor function, resulting from ataxia or epilepsy. The role that apparently normal proteins from these mutant genes play in these pathologies is not known. However, recent advances in previously known spinocerebellar ataxias originated by abnormal non-coding pentanucleotide repeats point to a gain of a toxic function by the pathogenic repeat-containing RNA that abnormally forms nuclear foci with RNA-binding proteins. In cells, RNA foci have been shown to be formed by phase separation. Moreover, the field of repeat expansions has lately achieved an extraordinary progress with the discovery that RNA repeats, polyglutamine, and polyalanine proteins are crucial for the formation of nuclear membraneless organelles by phase separation, which is perturbed when they are expanded. This review will cover the amazing advances on repeat diseases.
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Affiliation(s)
- Joana R. Loureiro
- Genetics of Cognitive Dysfunction Laboratory, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (J.R.L.); (A.F.C.); (A.S.F.)
- Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal
| | - Ana F. Castro
- Genetics of Cognitive Dysfunction Laboratory, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (J.R.L.); (A.F.C.); (A.S.F.)
- Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Ana S. Figueiredo
- Genetics of Cognitive Dysfunction Laboratory, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (J.R.L.); (A.F.C.); (A.S.F.)
- Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal
- Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Isabel Silveira
- Genetics of Cognitive Dysfunction Laboratory, i3S- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; (J.R.L.); (A.F.C.); (A.S.F.)
- Institute for Molecular and Cell Biology, Universidade do Porto, 4200-135 Porto, Portugal
- Correspondence: ; Tel.: +351-2240-8800
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33
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Annear DJ, Vandeweyer G, Sanchis-Juan A, Raymond FL, Kooy RF. Non-Mendelian inheritance patterns and extreme deviation rates of CGG repeats in autism. Genome Res 2022; 32:1967-1980. [PMID: 36351771 PMCID: PMC9808627 DOI: 10.1101/gr.277011.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/14/2022] [Indexed: 11/10/2022]
Abstract
As expansions of CGG short tandem repeats (STRs) are established as the genetic etiology of many neurodevelopmental disorders, we aimed to elucidate the inheritance patterns and role of CGG STRs in autism-spectrum disorder (ASD). By genotyping 6063 CGG STR loci in a large cohort of trios and quads with an ASD-affected proband, we determined an unprecedented rate of CGG repeat length deviation across a single generation. Although the concept of repeat length being linked to deviation rate was solidified, we show how shorter STRs display greater degrees of size variation. We observed that CGG STRs did not segregate by Mendelian principles but with a bias against longer repeats, which appeared to magnify as repeat length increased. Through logistic regression, we identified 19 genes that displayed significantly higher rates and degrees of CGG STR expansion within the ASD-affected probands (P < 1 × 10-5). This study not only highlights novel repeat expansions that may play a role in ASD but also reinforces the hypothesis that CGG STRs are specifically linked to human cognition.
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Affiliation(s)
- Dale J. Annear
- Department of Medical Genetics, University of Antwerp, 2600 Antwerp, Belgium
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, 2600 Antwerp, Belgium
| | - Alba Sanchis-Juan
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, United Kingdom;,Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Cambridge, CB2 0PT, United Kingdom
| | - F. Lucy Raymond
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, United Kingdom;,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, United Kingdom
| | - R. Frank Kooy
- Department of Medical Genetics, University of Antwerp, 2600 Antwerp, Belgium
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34
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Gall-Duncan T, Sato N, Yuen RKC, Pearson CE. Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences. Genome Res 2022; 32:1-27. [PMID: 34965938 PMCID: PMC8744678 DOI: 10.1101/gr.269530.120] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/29/2021] [Indexed: 11/25/2022]
Abstract
Expansions of gene-specific DNA tandem repeats (TRs), first described in 1991 as a disease-causing mutation in humans, are now known to cause >60 phenotypes, not just disease, and not only in humans. TRs are a common form of genetic variation with biological consequences, observed, so far, in humans, dogs, plants, oysters, and yeast. Repeat diseases show atypical clinical features, genetic anticipation, and multiple and partially penetrant phenotypes among family members. Discovery of disease-causing repeat expansion loci accelerated through technological advances in DNA sequencing and computational analyses. Between 2019 and 2021, 17 new disease-causing TR expansions were reported, totaling 63 TR loci (>69 diseases), with a likelihood of more discoveries, and in more organisms. Recent and historical lessons reveal that properly assessed clinical presentations, coupled with genetic and biological awareness, can guide discovery of disease-causing unstable TRs. We highlight critical but underrecognized aspects of TR mutations. Repeat motifs may not be present in current reference genomes but will be in forthcoming gapless long-read references. Repeat motif size can be a single nucleotide to kilobases/unit. At a given locus, repeat motif sequence purity can vary with consequence. Pathogenic repeats can be "insertions" within nonpathogenic TRs. Expansions, contractions, and somatic length variations of TRs can have clinical/biological consequences. TR instabilities occur in humans and other organisms. TRs can be epigenetically modified and/or chromosomal fragile sites. We discuss the expanding field of disease-associated TR instabilities, highlighting prospects, clinical and genetic clues, tools, and challenges for further discoveries of disease-causing TR instabilities and understanding their biological and pathological impacts-a vista that is about to expand.
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Affiliation(s)
- Terence Gall-Duncan
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Nozomu Sato
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
| | - Ryan K C Yuen
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Christopher E Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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35
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Deshmukh AL, Caron MC, Mohiuddin M, Lanni S, Panigrahi GB, Khan M, Engchuan W, Shum N, Faruqui A, Wang P, Yuen RKC, Nakamori M, Nakatani K, Masson JY, Pearson CE. FAN1 exo- not endo-nuclease pausing on disease-associated slipped-DNA repeats: A mechanism of repeat instability. Cell Rep 2021; 37:110078. [PMID: 34879276 DOI: 10.1016/j.celrep.2021.110078] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/02/2021] [Accepted: 11/09/2021] [Indexed: 12/19/2022] Open
Abstract
Ongoing inchworm-like CAG and CGG repeat expansions in brains, arising by aberrant processing of slipped DNAs, may drive Huntington's disease, fragile X syndrome, and autism. FAN1 nuclease modifies hyper-expansion rates by unknown means. We show that FAN1, through iterative cycles, binds, dimerizes, and cleaves slipped DNAs, yielding striking exo-nuclease pauses along slip-outs: 5'-C↓A↓GC↓A↓G-3' and 5'-C↓T↓G↓C↓T↓G-3'. CAG excision is slower than CTG and requires intra-strand A·A and T·T mismatches. Fully paired hairpins arrested excision, whereas disease-delaying CAA interruptions further slowed excision. Endo-nucleolytic cleavage is insensitive to slip-outs. Rare FAN1 variants are found in individuals with autism with CGG/CCG expansions, and CGG/CCG slip-outs show exo-nuclease pauses. The slip-out-specific ligand, naphthyridine-azaquinolone, which induces contractions of expanded repeats in vivo, requires FAN1 for its effect, and protects slip-outs from FAN1 exo-, but not endo-, nucleolytic digestion. FAN1's inchworm pausing of slip-out excision rates is well suited to modify inchworm expansion rates, which modify disease onset and progression.
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Affiliation(s)
- Amit Laxmikant Deshmukh
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Marie-Christine Caron
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Québec City, QC G1R 3S3, Canada; Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec City, QC G1R 3S3, Canada
| | - Mohiuddin Mohiuddin
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Stella Lanni
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Gagan B Panigrahi
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Mahreen Khan
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Program of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Worrawat Engchuan
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Natalie Shum
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Program of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Aisha Faruqui
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Program of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Peixiang Wang
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada
| | - Ryan K C Yuen
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Program of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Masayuki Nakamori
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, the Institute of Scientific and Industrial Research, Osaka University, Osaka 567-0047, Japan
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Québec City, QC G1R 3S3, Canada; Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University Cancer Research Center, Québec City, QC G1R 3S3, Canada
| | - Christopher E Pearson
- Program of Genetics & Genome Biology, The Hospital for Sick Children, PGCRL, Toronto, Canada, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Program of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
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36
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Schröder C, Horsthemke B, Depienne C. GC-rich repeat expansions: associated disorders and mechanisms. MED GENET-BERLIN 2021; 33:325-335. [PMID: 38835438 PMCID: PMC11006399 DOI: 10.1515/medgen-2021-2099] [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: 04/29/2021] [Accepted: 11/12/2021] [Indexed: 06/06/2024]
Abstract
Noncoding repeat expansions are a well-known cause of genetic disorders mainly affecting the central nervous system. Missed by most standard technologies used in routine diagnosis, pathogenic noncoding repeat expansions have to be searched for using specific techniques such as repeat-primed PCR or specific bioinformatics tools applied to genome data, such as ExpansionHunter. In this review, we focus on GC-rich repeat expansions, which represent at least one third of all noncoding repeat expansions described so far. GC-rich expansions are mainly located in regulatory regions (promoter, 5' untranslated region, first intron) of genes and can lead to either a toxic gain-of-function mediated by RNA toxicity and/or repeat-associated non-AUG (RAN) translation, or a loss-of-function of the associated gene, depending on their size and their methylation status. We herein review the clinical and molecular characteristics of disorders associated with these difficult-to-detect expansions.
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Affiliation(s)
- Christopher Schröder
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Bernhard Horsthemke
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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37
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Natural selection at the RASGEF1C (GGC) repeat in human and divergent genotypes in late-onset neurocognitive disorder. Sci Rep 2021; 11:19235. [PMID: 34584172 PMCID: PMC8479062 DOI: 10.1038/s41598-021-98725-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 09/14/2021] [Indexed: 12/17/2022] Open
Abstract
Expression dysregulation of the neuron-specific gene, RASGEF1C (RasGEF Domain Family Member 1C), occurs in late-onset neurocognitive disorders (NCDs), such as Alzheimer's disease. This gene contains a (GGC)13, spanning its core promoter and 5' untranslated region (RASGEF1C-201 ENST00000361132.9). Here we sequenced the (GGC)-repeat in a sample of human subjects (N = 269), consisting of late-onset NCDs (N = 115) and controls (N = 154). We also studied the status of this STR across various primate and non-primate species based on Ensembl 103. The 6-repeat allele was the predominant allele in the controls (frequency = 0.85) and NCD patients (frequency = 0.78). The NCD genotype compartment consisted of an excess of genotypes that lacked the 6-repeat (divergent genotypes) (Mid-P exact = 0.004). A number of those genotypes were not detected in the control group (Mid-P exact = 0.007). The RASGEF1C (GGC)-repeat expanded beyond 2-repeats specifically in primates, and was at maximum length in human. We conclude that there is natural selection for the 6-repeat allele of the RASGEF1C (GGC)-repeat in human, and significant divergence from that allele in late-onset NCDs. STR alleles that are predominantly abundant and genotypes that deviate from those alleles are underappreciated features, which may have deep evolutionary and pathological consequences.
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38
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Mizumoto S, Yamada S. Congenital Disorders of Deficiency in Glycosaminoglycan Biosynthesis. Front Genet 2021; 12:717535. [PMID: 34539746 PMCID: PMC8446454 DOI: 10.3389/fgene.2021.717535] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/12/2021] [Indexed: 12/04/2022] Open
Abstract
Glycosaminoglycans (GAGs) including chondroitin sulfate, dermatan sulfate, and heparan sulfate are covalently attached to specific core proteins to form proteoglycans, which are distributed at the cell surface as well as in the extracellular matrix. Proteoglycans and GAGs have been demonstrated to exhibit a variety of physiological functions such as construction of the extracellular matrix, tissue development, and cell signaling through interactions with extracellular matrix components, morphogens, cytokines, and growth factors. Not only connective tissue disorders including skeletal dysplasia, chondrodysplasia, multiple exostoses, and Ehlers-Danlos syndrome, but also heart and kidney defects, immune deficiencies, and neurological abnormalities have been shown to be caused by defects in GAGs as well as core proteins of proteoglycans. These findings indicate that GAGs and proteoglycans are essential for human development in major organs. The glycobiological aspects of congenital disorders caused by defects in GAG-biosynthetic enzymes including specific glysocyltransferases, epimerases, and sulfotransferases, in addition to core proteins of proteoglycans will be comprehensively discussed based on the literature to date.
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Affiliation(s)
- Shuji Mizumoto
- Department of Pathobiochemistry, Faculty of Pharmacy, Meijo University, Nagoya, Japan
| | - Shuhei Yamada
- Department of Pathobiochemistry, Faculty of Pharmacy, Meijo University, Nagoya, Japan
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39
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Luperchio TR, Boukas L, Zhang L, Pilarowski G, Jiang J, Kalinousky A, Hansen KD, Bjornsson HT. Leveraging the Mendelian disorders of the epigenetic machinery to systematically map functional epigenetic variation. eLife 2021; 10:65884. [PMID: 34463256 PMCID: PMC8443249 DOI: 10.7554/elife.65884] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 08/27/2021] [Indexed: 12/12/2022] Open
Abstract
Although each Mendelian Disorder of the Epigenetic Machinery (MDEM) has a different causative gene, there are shared disease manifestations. We hypothesize that this phenotypic convergence is a consequence of shared epigenetic alterations. To identify such shared alterations, we interrogate chromatin (ATAC-seq) and expression (RNA-seq) states in B cells from three MDEM mouse models (Kabuki [KS] type 1 and 2 and Rubinstein-Taybi type 1 [RT1] syndromes). We develop a new approach for the overlap analysis and find extensive overlap primarily localized in gene promoters. We show that disruption of chromatin accessibility at promoters often disrupts downstream gene expression, and identify 587 loci and 264 genes with shared disruption across all three MDEMs. Subtle expression alterations of multiple, IgA-relevant genes, collectively contribute to IgA deficiency in KS1 and RT1, but not in KS2. We propose that the joint study of MDEMs offers a principled approach for systematically mapping functional epigenetic variation in mammals.
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Affiliation(s)
- Teresa Romeo Luperchio
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Leandros Boukas
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Li Zhang
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Genay Pilarowski
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Jenny Jiang
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Allison Kalinousky
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Kasper D Hansen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, United States
| | - Hans T Bjornsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Landspitali University Hospital, Reykjavik, Iceland
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40
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Miller DE, Sulovari A, Wang T, Loucks H, Hoekzema K, Munson KM, Lewis AP, Fuerte EPA, Paschal CR, Walsh T, Thies J, Bennett JT, Glass I, Dipple KM, Patterson K, Bonkowski ES, Nelson Z, Squire A, Sikes M, Beckman E, Bennett RL, Earl D, Lee W, Allikmets R, Perlman SJ, Chow P, Hing AV, Wenger TL, Adam MP, Sun A, Lam C, Chang I, Zou X, Austin SL, Huggins E, Safi A, Iyengar AK, Reddy TE, Majoros WH, Allen AS, Crawford GE, Kishnani PS, King MC, Cherry T, Chong JX, Bamshad MJ, Nickerson DA, Mefford HC, Doherty D, Eichler EE. Targeted long-read sequencing identifies missing disease-causing variation. Am J Hum Genet 2021; 108:1436-1449. [PMID: 34216551 PMCID: PMC8387463 DOI: 10.1016/j.ajhg.2021.06.006] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/07/2021] [Indexed: 12/28/2022] Open
Abstract
Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-evaluate structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted. We performed targeted long-read sequencing (T-LRS) using adaptive sampling on the Oxford Nanopore platform on 40 individuals, 10 of whom lacked a complete molecular diagnosis. We computationally targeted up to 151 Mbp of sequence per individual and searched for pathogenic substitutions, structural variants, and methylation differences using a single data source. We detected all genomic aberrations-including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences-identified by prior clinical testing. In 8/8 individuals with complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, leading to changes in clinical management in one case. In ten individuals with suspected Mendelian conditions lacking a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in six and variants of uncertain significance in two others. T-LRS accurately identifies pathogenic structural variants, resolves complex rearrangements, and identifies Mendelian variants not detected by other technologies. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority genes and regions or complex clinical testing results.
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Affiliation(s)
- Danny E Miller
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA.
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Hailey Loucks
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Edith P Almanza Fuerte
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Catherine R Paschal
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Tom Walsh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jenny Thies
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - James T Bennett
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Department of Laboratories, Seattle Children's Hospital, Seattle, WA 98105, USA; Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Ian Glass
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Katrina M Dipple
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Karynne Patterson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Emily S Bonkowski
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Zoe Nelson
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Audrey Squire
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Megan Sikes
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Erika Beckman
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Robin L Bennett
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Dawn Earl
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Winston Lee
- Department of Genetics and Development, Columbia University, New York, NY 10032, USA; Department of Ophthalmology, Columbia University, New York, NY 10032, USA
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University, New York, NY 10032, USA
| | - Seth J Perlman
- Department of Neurology, Seattle Children's Hospital, University of Washington, Seattle, WA 98105, USA
| | - Penny Chow
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98195, USA
| | - Anne V Hing
- Department of Pediatrics, Division of Craniofacial Medicine, University of Washington, Seattle, WA 98195, USA
| | - Tara L Wenger
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Margaret P Adam
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Angela Sun
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Center for Clinical and Translational Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Christina Lam
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Irene Chang
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Xue Zou
- Program in Computational Biology & Bioinformatics, Duke University, Durham, NC 27710, USA
| | - Stephanie L Austin
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Erin Huggins
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Alexias Safi
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Apoorva K Iyengar
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA; University Program in Genetics and Genomics, Duke University; Durham, NC 27708, USA
| | - Timothy E Reddy
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - William H Majoros
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - Andrew S Allen
- Department of Biostatistics and Bioinformatics, Duke University; Durham, NC 27708, USA
| | - Gregory E Crawford
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Priya S Kishnani
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27708, USA
| | - Mary-Claire King
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Tim Cherry
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Jessica X Chong
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Dan Doherty
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Department of Pediatrics, Division of Developmental Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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41
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The evolving genetic landscape of congenital disorders of glycosylation. Biochim Biophys Acta Gen Subj 2021; 1865:129976. [PMID: 34358634 DOI: 10.1016/j.bbagen.2021.129976] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/30/2021] [Indexed: 01/01/2023]
Abstract
Congenital Disorders of Glycosylation (CDG) are an expanding and complex group of rare genetic disorders caused by defects in the glycosylation of proteins and lipids. The genetic spectrum of CDG is extremely broad with mutations in over 140 genes leading to a wide variety of symptoms ranging from mild to severe and life-threatening. There has been an expansion in the genetic complexity of CDG in recent years. More specifically several examples of alternate phenotypes in recessive forms of CDG and new types of CDG following an autosomal dominant inheritance pattern have been identified. In addition, novel genetic mechanisms such as expansion repeats have been reported and several already known disorders have been classified as CDG as their pathophysiology was better elucidated. Furthermore, we consider the future and outlook of CDG genetics, with a focus on exploration of the non-coding genome using whole genome sequencing, RNA-seq and multi-omics technology.
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42
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Seaby EG, Rehm HL, O’Donnell-Luria A. Strategies to Uplift Novel Mendelian Gene Discovery for Improved Clinical Outcomes. Front Genet 2021; 12:674295. [PMID: 34220947 PMCID: PMC8248347 DOI: 10.3389/fgene.2021.674295] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/12/2021] [Indexed: 01/31/2023] Open
Abstract
Rare genetic disorders, while individually rare, are collectively common. They represent some of the most severe disorders affecting patients worldwide with significant morbidity and mortality. Over the last decade, advances in genomic methods have significantly uplifted diagnostic rates for patients and facilitated novel and targeted therapies. However, many patients with rare genetic disorders still remain undiagnosed as the genetic etiology of only a proportion of Mendelian conditions has been discovered to date. This article explores existing strategies to identify novel Mendelian genes and how these discoveries impact clinical care and therapeutics. We discuss the importance of data sharing, phenotype-driven approaches, patient-led approaches, utilization of large-scale genomic sequencing projects, constraint-based methods, integration of multi-omics data, and gene-to-patient methods. We further consider the health economic advantages of novel gene discovery and speculate on potential future methods for improved clinical outcomes.
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Affiliation(s)
- Eleanor G. Seaby
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Genomic Informatics Group, University Hospital Southampton, Southampton, United Kingdom
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, United States
| | - Heidi L. Rehm
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States
| | - Anne O’Donnell-Luria
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Center for Genomic Medicine, Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, United States
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, United States
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA, United States
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43
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Dubail J, Cormier-Daire V. Chondrodysplasias With Multiple Dislocations Caused by Defects in Glycosaminoglycan Synthesis. Front Genet 2021; 12:642097. [PMID: 34220933 PMCID: PMC8242584 DOI: 10.3389/fgene.2021.642097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Chondrodysplasias with multiple dislocations form a group of severe disorders characterized by joint laxity and multiple dislocations, severe short stature of pre- and post-natal onset, hand anomalies, and/or vertebral anomalies. The majority of chondrodysplasias with multiple dislocations have been associated with mutations in genes encoding glycosyltransferases, sulfotransferases, and transporters implicated in the synthesis or sulfation of glycosaminoglycans, long and unbranched polysaccharides composed of repeated disaccharide bond to protein core of proteoglycan. Glycosaminoglycan biosynthesis is a tightly regulated process that occurs mainly in the Golgi and that requires the coordinated action of numerous enzymes and transporters as well as an adequate Golgi environment. Any disturbances of this chain of reactions will lead to the incapacity of a cell to construct correct glycanic chains. This review focuses on genetic and glycobiological studies of chondrodysplasias with multiple dislocations associated with glycosaminoglycan biosynthesis defects and related animal models. Strong comprehension of the molecular mechanisms leading to those disorders, mostly through extensive phenotypic analyses of in vitro and/or in vivo models, is essential for the development of novel biomarkers for clinical screenings and innovative therapeutics for these diseases.
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Affiliation(s)
- Johanne Dubail
- Université de Paris, INSERM UMR 1163, Institut Imagine, Paris, France
| | - Valérie Cormier-Daire
- Université de Paris, INSERM UMR 1163, Institut Imagine, Paris, France.,Service de Génétique Clinique, Centre de Référence Pour Les Maladies Osseuses Constitutionnelles, AP-HP, Hôpital Necker-Enfants Malades, Paris, France
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44
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Chintalaphani SR, Pineda SS, Deveson IW, Kumar KR. An update on the neurological short tandem repeat expansion disorders and the emergence of long-read sequencing diagnostics. Acta Neuropathol Commun 2021; 9:98. [PMID: 34034831 PMCID: PMC8145836 DOI: 10.1186/s40478-021-01201-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/17/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Short tandem repeat (STR) expansion disorders are an important cause of human neurological disease. They have an established role in more than 40 different phenotypes including the myotonic dystrophies, Fragile X syndrome, Huntington's disease, the hereditary cerebellar ataxias, amyotrophic lateral sclerosis and frontotemporal dementia. MAIN BODY STR expansions are difficult to detect and may explain unsolved diseases, as highlighted by recent findings including: the discovery of a biallelic intronic 'AAGGG' repeat in RFC1 as the cause of cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS); and the finding of 'CGG' repeat expansions in NOTCH2NLC as the cause of neuronal intranuclear inclusion disease and a range of clinical phenotypes. However, established laboratory techniques for diagnosis of repeat expansions (repeat-primed PCR and Southern blot) are cumbersome, low-throughput and poorly suited to parallel analysis of multiple gene regions. While next generation sequencing (NGS) has been increasingly used, established short-read NGS platforms (e.g., Illumina) are unable to genotype large and/or complex repeat expansions. Long-read sequencing platforms recently developed by Oxford Nanopore Technology and Pacific Biosciences promise to overcome these limitations to deliver enhanced diagnosis of repeat expansion disorders in a rapid and cost-effective fashion. CONCLUSION We anticipate that long-read sequencing will rapidly transform the detection of short tandem repeat expansion disorders for both clinical diagnosis and gene discovery.
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Affiliation(s)
- Sanjog R. Chintalaphani
- School of Medicine, University of New South Wales, Sydney, 2052 Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
| | - Sandy S. Pineda
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
- Brain and Mind Centre, University of Sydney, Camperdown, NSW 2050 Australia
| | - Ira W. Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
- Faculty of Medicine, St Vincent’s Clinical School, University of New South Wales, Sydney, NSW 2010 Australia
| | - Kishore R. Kumar
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010 Australia
- Molecular Medicine Laboratory and Neurology Department, Central Clinical School, Concord Repatriation General Hospital, University of Sydney, Concord, NSW 2137 Australia
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45
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Depienne C, Mandel JL. 30 years of repeat expansion disorders: What have we learned and what are the remaining challenges? Am J Hum Genet 2021; 108:764-785. [PMID: 33811808 PMCID: PMC8205997 DOI: 10.1016/j.ajhg.2021.03.011] [Citation(s) in RCA: 162] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/05/2021] [Indexed: 12/13/2022] Open
Abstract
Tandem repeats represent one of the most abundant class of variations in human genomes, which are polymorphic by nature and become highly unstable in a length-dependent manner. The expansion of repeat length across generations is a well-established process that results in human disorders mainly affecting the central nervous system. At least 50 disorders associated with expansion loci have been described to date, with half recognized only in the last ten years, as prior methodological difficulties limited their identification. These limitations still apply to the current widely used molecular diagnostic methods (exome or gene panels) and thus result in missed diagnosis detrimental to affected individuals and their families, especially for disorders that are very rare and/or clinically not recognizable. Most of these disorders have been identified through family-driven approaches and many others likely remain to be identified. The recent development of long-read technologies provides a unique opportunity to systematically investigate the contribution of tandem repeats and repeat expansions to the genetic architecture of human disorders. In this review, we summarize the current and most recent knowledge about the genetics of repeat expansion disorders and the diversity of their pathophysiological mechanisms and outline the perspectives of developing personalized treatments in the future.
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Affiliation(s)
- Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany; Institut du Cerveau et de la Moelle épinière (ICM), Sorbonne Université, UMR S 1127, Inserm U1127, CNRS UMR 7225, 75013 Paris, France.
| | - Jean-Louis Mandel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch 67400, France; Centre National de la Recherche Scientifique, UMR 7104, Illkirch 67400, France; Institut National de la Santé et de la Recherche Médicale, U 1258, Illkirch 67400, France; Université de Strasbourg, Illkirch 67400, France; USIAS University of Strasbourg Institute of Advanced study, 67000 Strasbourg, France.
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46
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Gusic M, Prokisch H. Genetic basis of mitochondrial diseases. FEBS Lett 2021; 595:1132-1158. [PMID: 33655490 DOI: 10.1002/1873-3468.14068] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 12/13/2022]
Abstract
Mitochondrial disorders are monogenic disorders characterized by a defect in oxidative phosphorylation and caused by pathogenic variants in one of over 340 different genes. The implementation of whole-exome sequencing has led to a revolution in their diagnosis, duplicated the number of associated disease genes, and significantly increased the diagnosed fraction. However, the genetic etiology of a substantial fraction of patients exhibiting mitochondrial disorders remains unknown, highlighting limitations in variant detection and interpretation, which calls for improved computational and DNA sequencing methods, as well as the addition of OMICS tools. More intriguingly, this also suggests that some pathogenic variants lie outside of the protein-coding genes and that the mechanisms beyond the Mendelian inheritance and the mtDNA are of relevance. This review covers the current status of the genetic basis of mitochondrial diseases, discusses current challenges and perspectives, and explores the contribution of factors beyond the protein-coding regions and monogenic inheritance in the expansion of the genetic spectrum of disease.
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Affiliation(s)
- Mirjana Gusic
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technical University of Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Germany
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technical University of Munich, Germany
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47
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Mechanisms of repeat-associated non-AUG translation in neurological microsatellite expansion disorders. Biochem Soc Trans 2021; 49:775-792. [PMID: 33729487 PMCID: PMC8106499 DOI: 10.1042/bst20200690] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 02/20/2021] [Accepted: 02/23/2021] [Indexed: 02/08/2023]
Abstract
Repeat-associated non-AUG (RAN) translation was discovered in 2011 in spinocerebellar ataxia type 8 (SCA8) and myotonic dystrophy type 1 (DM1). This non-canonical form of translation occurs in all reading frames from both coding and non-coding regions of sense and antisense transcripts carrying expansions of trinucleotide to hexanucleotide repeat sequences. RAN translation has since been reported in 7 of the 53 known microsatellite expansion disorders which mainly present with neurodegenerative features. RAN translation leads to the biosynthesis of low-complexity polymeric repeat proteins with aggregating and cytotoxic properties. However, the molecular mechanisms and protein factors involved in assembling functional ribosomes in absence of canonical AUG start codons remain poorly characterised while secondary repeat RNA structures play key roles in initiating RAN translation. Here, we briefly review the repeat expansion disorders, their complex pathogenesis and the mechanisms of physiological translation initiation together with the known factors involved in RAN translation. Finally, we discuss research challenges surrounding the understanding of pathogenesis and future directions that may provide opportunities for the development of novel therapeutic approaches for this group of incurable neurodegenerative diseases.
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48
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Annear DJ, Vandeweyer G, Elinck E, Sanchis-Juan A, French CE, Raymond L, Kooy RF. Abundancy of polymorphic CGG repeats in the human genome suggest a broad involvement in neurological disease. Sci Rep 2021; 11:2515. [PMID: 33510257 PMCID: PMC7844047 DOI: 10.1038/s41598-021-82050-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/29/2020] [Indexed: 11/09/2022] Open
Abstract
Expanded CGG-repeats have been linked to neurodevelopmental and neurodegenerative disorders, including the fragile X syndrome and fragile X-associated tremor/ataxia syndrome (FXTAS). We hypothesized that as of yet uncharacterised CGG-repeat expansions within the genome contribute to human disease. To catalogue the CGG-repeats, 544 human whole genomes were analyzed. In total, 6101 unique CGG-repeats were detected of which more than 93% were highly variable in repeat length. Repeats with a median size of 12 repeat units or more were always polymorphic but shorter repeats were often polymorphic, suggesting a potential intergenerational instability of the CGG region even for repeats units with a median length of four or less. 410 of the CGG repeats were associated with known neurodevelopmental disease genes or with strong candidate genes. Based on their frequency and genomic location, CGG repeats may thus be a currently overlooked cause of human disease.
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Affiliation(s)
- Dale J Annear
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Ellen Elinck
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Alba Sanchis-Juan
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.,Department of Haematology, NHS Blood and Transplant Centre, University of Cambridge, Cambridge, CB2 0PT, UK
| | - Courtney E French
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Lucy Raymond
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.
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49
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Monckton DG. The Contribution of Somatic Expansion of the CAG Repeat to Symptomatic Development in Huntington's Disease: A Historical Perspective. J Huntingtons Dis 2021; 10:7-33. [PMID: 33579863 PMCID: PMC7990401 DOI: 10.3233/jhd-200429] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The discovery in the early 1990s of the expansion of unstable simple sequence repeats as the causative mutation for a number of inherited human disorders, including Huntington's disease (HD), opened up a new era of human genetics and provided explanations for some old problems. In particular, an inverse association between the number of repeats inherited and age at onset, and unprecedented levels of germline instability, biased toward further expansion, provided an explanation for the wide symptomatic variability and anticipation observed in HD and many of these disorders. The repeats were also revealed to be somatically unstable in a process that is expansion-biased, age-dependent and tissue-specific, features that are now increasingly recognised as contributory to the age-dependence, progressive nature and tissue specificity of the symptoms of HD, and at least some related disorders. With much of the data deriving from affected individuals, and model systems, somatic expansions have been revealed to arise in a cell division-independent manner in critical target tissues via a mechanism involving key components of the DNA mismatch repair pathway. These insights have opened new approaches to thinking about how the disease could be treated by suppressing somatic expansion and revealed novel protein targets for intervention. Exciting times lie ahead in turning these insights into novel therapies for HD and related disorders.
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Affiliation(s)
- Darren G. Monckton
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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50
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Jaeken J. Congenital disorders of glycosylation: A multi-genetic disease family with multiple subcellular locations. JOURNAL OF MOTHER AND CHILD 2020; 24:14-20. [PMID: 33554500 PMCID: PMC8518092 DOI: 10.34763/jmotherandchild.20202402si.2005.000004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This review discusses a selection of congenital disorders of glycosylation that show peculiar features, such as an unusual presentation, different phenotypes, a novel biochemical/genetic mechanism, a relatively high frequency or a relatively efficient treatment.
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Affiliation(s)
- Jaak Jaeken
- Department of Development and Regeneration, Center for Metabolic Diseases, University Hospital Gasthuisberg, KU Leuven, Leuven, Belgium
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