1
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Reis ALM, Rapadas M, Hammond JM, Gamaarachchi H, Stevanovski I, Ayuputeri Kumaheri M, Chintalaphani SR, Dissanayake DSB, Siggs OM, Hewitt AW, Llamas B, Brown A, Baynam G, Mann GJ, McMorran BJ, Easteal S, Hermes A, Jenkins MR, Patel HR, Deveson IW. The landscape of genomic structural variation in Indigenous Australians. Nature 2023; 624:602-610. [PMID: 38093003 PMCID: PMC10733147 DOI: 10.1038/s41586-023-06842-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 11/07/2023] [Indexed: 12/20/2023]
Abstract
Indigenous Australians harbour rich and unique genomic diversity. However, Aboriginal and Torres Strait Islander ancestries are historically under-represented in genomics research and almost completely missing from reference datasets1-3. Addressing this representation gap is critical, both to advance our understanding of global human genomic diversity and as a prerequisite for ensuring equitable outcomes in genomic medicine. Here we apply population-scale whole-genome long-read sequencing4 to profile genomic structural variation across four remote Indigenous communities. We uncover an abundance of large insertion-deletion variants (20-49 bp; n = 136,797), structural variants (50 b-50 kb; n = 159,912) and regions of variable copy number (>50 kb; n = 156). The majority of variants are composed of tandem repeat or interspersed mobile element sequences (up to 90%) and have not been previously annotated (up to 62%). A large fraction of structural variants appear to be exclusive to Indigenous Australians (12% lower-bound estimate) and most of these are found in only a single community, underscoring the need for broad and deep sampling to achieve a comprehensive catalogue of genomic structural variation across the Australian continent. Finally, we explore short tandem repeats throughout the genome to characterize allelic diversity at 50 known disease loci5, uncover hundreds of novel repeat expansion sites within protein-coding genes, and identify unique patterns of diversity and constraint among short tandem repeat sequences. Our study sheds new light on the dimensions and dynamics of genomic structural variation within and beyond Australia.
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Affiliation(s)
- Andre L M Reis
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Melissa Rapadas
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
| | - Jillian M Hammond
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
| | - Hasindu Gamaarachchi
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
- School of Computer Science and Engineering, University of New South Wales, Sydney, New South Wales, Australia
| | - Igor Stevanovski
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
| | - Meutia Ayuputeri Kumaheri
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
| | - Sanjog R Chintalaphani
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Duminda S B Dissanayake
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Institute for Applied Ecology, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - Owen M Siggs
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
- Department of Ophthalmology, Flinders University, Bedford Park, South Australia, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Bastien Llamas
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Australian Centre for Ancient DNA, School of Biological Sciences and Environment Institute, University of Adelaide, Adelaide, South Australia, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, South Australia, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, South Australia, Australia
| | - Alex Brown
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, South Australia, Australia
| | - Gareth Baynam
- Telethon Kids Institute and Division of Paediatrics, Faculty of Health and Medical Sciences, University of Western Australia, Perth, Western Australia, Australia
- Genetic Services of Western Australia, Western Australian Department of Health, Perth, Western Australia, Australia
- Western Australian Register of Developmental Anomalies, Western Australian Department of Health, Perth, Western Australia, Australia
| | - Graham J Mann
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Brendan J McMorran
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Simon Easteal
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Azure Hermes
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Misty R Jenkins
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Hardip R Patel
- National Centre for Indigenous Genomics, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia.
| | - Ira W Deveson
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia.
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia.
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2
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Dominik N, Magri S, Currò R, Abati E, Facchini S, Corbetta M, Macpherson H, Di Bella D, Sarto E, Stevanovski I, Chintalaphani SR, Akcimen F, Manini A, Vegezzi E, Quartesan I, Montgomery KA, Pirota V, Crespan E, Perini C, Grupelli GP, Tomaselli PJ, Marques W, Shaw J, Polke J, Salsano E, Fenu S, Pareyson D, Pisciotta C, Tofaris GK, Nemeth AH, Ealing J, Radunovic A, Kearney S, Kumar KR, Vucic S, Kennerson M, Reilly MM, Houlden H, Deveson I, Tucci A, Taroni F, Cortese A. Normal and pathogenic variation of RFC1 repeat expansions: implications for clinical diagnosis. Brain 2023; 146:5060-5069. [PMID: 37450567 PMCID: PMC10689911 DOI: 10.1093/brain/awad240] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/11/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023] Open
Abstract
Cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS) is an autosomal recessive neurodegenerative disease, usually caused by biallelic AAGGG repeat expansions in RFC1. In this study, we leveraged whole genome sequencing data from nearly 10 000 individuals recruited within the Genomics England sequencing project to investigate the normal and pathogenic variation of the RFC1 repeat. We identified three novel repeat motifs, AGGGC (n = 6 from five families), AAGGC (n = 2 from one family) and AGAGG (n = 1), associated with CANVAS in the homozygous or compound heterozygous state with the common pathogenic AAGGG expansion. While AAAAG, AAAGGG and AAGAG expansions appear to be benign, we revealed a pathogenic role for large AAAGG repeat configuration expansions (n = 5). Long-read sequencing was used to characterize the entire repeat sequence, and six patients exhibited a pure AGGGC expansion, while the other patients presented complex motifs with AAGGG or AAAGG interruptions. All pathogenic motifs appeared to have arisen from a common haplotype and were predicted to form highly stable G quadruplexes, which have previously been demonstrated to affect gene transcription in other conditions. The assessment of these novel configurations is warranted in CANVAS patients with negative or inconclusive genetic testing. Particular attention should be paid to carriers of compound AAGGG/AAAGG expansions when the AAAGG motif is very large (>500 repeats) or the AAGGG motif is interrupted. Accurate sizing and full sequencing of the satellite repeat with long-read sequencing is recommended in clinically selected cases to enable accurate molecular diagnosis and counsel patients and their families.
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Affiliation(s)
- Natalia Dominik
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Stefania Magri
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, Milan 20133, Italy
| | - Riccardo Currò
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of
Pavia, Pavia 27100, Italy
| | - Elena Abati
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
- Department of Pathophysiology and Transplantation, University of
Milan, Milan 20122, Italy
| | - Stefano Facchini
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
- IRCCS Mondino Foundation, Pavia 27100,
Italy
| | - Marinella Corbetta
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, Milan 20133, Italy
| | - Hannah Macpherson
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Daniela Di Bella
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, Milan 20133, Italy
| | - Elisa Sarto
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, Milan 20133, Italy
| | - Igor Stevanovski
- Genomics Pillar, Garvan Institute of Medical Research,
Sydney 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and
Murdoch Children’s Research Institute, Darlinghurst
2010, Australia
| | - Sanjog R Chintalaphani
- Centre for Population Genomics, Garvan Institute of Medical Research and
Murdoch Children’s Research Institute, Darlinghurst
2010, Australia
| | - Fulya Akcimen
- Laboratory of Neurogenetics, National Institute on Aging, National
Institutes of Health, Bethesda, MD 2292, USA
| | - Arianna Manini
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
- Department of Pathophysiology and Transplantation, University of
Milan, Milan 20122, Italy
- Department of Neurology and Laboratory of Neuroscience, IRCCS Istituto
Auxologico Italiano, Milan 20145, Italy
| | | | - Ilaria Quartesan
- Department of Brain and Behavioral Sciences, University of
Pavia, Pavia 27100, Italy
| | - Kylie-Ann Montgomery
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Valentina Pirota
- Department of Chemistry, University of Pavia,
Pavia 27100, Italy
- G4-INTERACT, USERN, 27100 Pavia,
Italy
| | - Emmanuele Crespan
- Institute of Molecular Genetics IGM-CNR ‘Luigi Luca
Cavalli-Sforza’, Pavia 27100, Italy
| | - Cecilia Perini
- Institute of Molecular Genetics IGM-CNR ‘Luigi Luca
Cavalli-Sforza’, Pavia 27100, Italy
| | - Glenda Paola Grupelli
- Institute of Molecular Genetics IGM-CNR ‘Luigi Luca
Cavalli-Sforza’, Pavia 27100, Italy
| | - Pedro J Tomaselli
- Department of Neurology, School of Medicine of Ribeirão Preto, University
of São Paulo, Ribeirão Preto 2650, Brazil
| | - Wilson Marques
- Department of Neurology, School of Medicine of Ribeirão Preto, University
of São Paulo, Ribeirão Preto 2650, Brazil
| | - Joseph Shaw
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - James Polke
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Ettore Salsano
- Clinic of Central and Peripheral Degenerative Neuropathies Unit, IRCCS
Foundation, C. Besta Neurological Institute, Milan
20126, Italy
| | - Silvia Fenu
- Clinic of Central and Peripheral Degenerative Neuropathies Unit, IRCCS
Foundation, C. Besta Neurological Institute, Milan
20126, Italy
| | - Davide Pareyson
- Clinic of Central and Peripheral Degenerative Neuropathies Unit, IRCCS
Foundation, C. Besta Neurological Institute, Milan
20126, Italy
| | - Chiara Pisciotta
- Clinic of Central and Peripheral Degenerative Neuropathies Unit, IRCCS
Foundation, C. Besta Neurological Institute, Milan
20126, Italy
| | - George K Tofaris
- Nuffield Department of Clinical Neurosciences, University of
Oxford, Oxford OX3 9DU, UK
| | - Andrea H Nemeth
- Nuffield Department of Clinical Neurosciences, University of
Oxford, Oxford OX3 9DU, UK
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS
Foundation Trust, Oxford OX3 7HE, UK
| | - John Ealing
- Salford Royal NHS Foundation Trust Greater Manchester Neuroscience Centre,
Manchester Centre for Clinical Neurosciences Salford, Greater
Manchester M6 8HD, UK
| | | | - Seamus Kearney
- Department of Neurology, Royal Victoria Hospital,
Belfast BT12 6BA, UK
| | - Kishore R Kumar
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical
Research, Darlinghurst, NSW 2010, Australia
- Molecular Medicine Laboratory, Concord Hospital,
Concord, NSW 2139, Australia
- Concord Clinical School, Faculty of Medicine and Health, University of
Sydney, Sydney, NSW 2139, Australia
| | - Steve Vucic
- Concord Clinical School, Faculty of Medicine and Health, University of
Sydney, Sydney, NSW 2139, Australia
- Brain and Nerve Research Centre, Concord Hospital,
Sydney, NSW 2139, Australia
| | - Marina Kennerson
- Molecular Medicine Laboratory, Concord Hospital,
Concord, NSW 2139, Australia
- Northcott Neuroscience Laboratory, ANZAC Research Institute
SLHD, Sydney, NSW 2050, Australia
- School of Medical Sciences, Faculty of Medicine and Health, University of
Sydney, Sydney, NSW 2050, Australia
| | - Mary M Reilly
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Ira Deveson
- Genomics Pillar, Garvan Institute of Medical Research,
Sydney 2010, Australia
| | - Arianna Tucci
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
| | - Franco Taroni
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto
Neurologico Carlo Besta, Milan 20133, Italy
| | - Andrea Cortese
- Department of Neuromuscular Diseases, University College
London, London WC1N 3BG, UK
- Department of Brain and Behavioral Sciences, University of
Pavia, Pavia 27100, Italy
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3
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Scriba CK, Stevanovski I, Chintalaphani SR, Gamaarachchi H, Ghaoui R, Ghia D, Henderson RD, Jordan N, Winkel A, Lamont PJ, Rodrigues MJ, Roxburgh RH, Weisburd B, Laing NG, Deveson IW, Davis MR, Ravenscroft G. RFC1 in an Australasian neurological disease cohort: extending the genetic heterogeneity and implications for diagnostics. Brain Commun 2023; 5:fcad208. [PMID: 37621409 PMCID: PMC10445415 DOI: 10.1093/braincomms/fcad208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/04/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Cerebellar ataxia, neuropathy and vestibular areflexia syndrome is a progressive, generally late-onset, neurological disorder associated with biallelic pentanucleotide expansions in Intron 2 of the RFC1 gene. The locus exhibits substantial genetic variability, with multiple pathogenic and benign pentanucleotide repeat alleles previously identified. To determine the contribution of pathogenic RFC1 expansions to neurological disease within an Australasian cohort and further investigate the heterogeneity exhibited at the locus, a combination of flanking and repeat-primed PCR was used to screen a cohort of 242 Australasian patients with neurological disease. Patients whose data indicated large gaps within expanded alleles following repeat-primed PCR, underwent targeted long-read sequencing to identify novel repeat motifs at the locus. To increase diagnostic yield, additional probes at the RFC1 repeat region were incorporated into the PathWest diagnostic laboratory targeted neurological disease gene panel to enable first-pass screening of the locus for all samples tested on the panel. Within the Australasian cohort, we detected known pathogenic biallelic expansions in 15.3% (n = 37) of patients. Thirty indicated biallelic AAGGG expansions, two had biallelic 'Māori alleles' [(AAAGG)exp(AAGGG)exp], two samples were compound heterozygous for the Māori allele and an AAGGG expansion, two samples had biallelic ACAGG expansions and one sample was compound heterozygous for the ACAGG and AAGGG expansions. Forty-five samples tested indicated the presence of biallelic expansions not known to be pathogenic. A large proportion (84%) showed complex interrupted patterns following repeat-primed PCR, suggesting that these expansions are likely to be comprised of more than one repeat motif, including previously unknown repeats. Using targeted long-read sequencing, we identified three novel repeat motifs in expanded alleles. Here, we also show that short-read sequencing can be used to reliably screen for the presence or absence of biallelic RFC1 expansions in all samples tested using the PathWest targeted neurological disease gene panel. Our results show that RFC1 pathogenic expansions make a substantial contribution to neurological disease in the Australasian population and further extend the heterogeneity of the locus. To accommodate the increased complexity, we outline a multi-step workflow utilizing both targeted short- and long-read sequencing to achieve a definitive genotype and provide accurate diagnoses for patients.
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Affiliation(s)
- Carolin K Scriba
- Rare Genetic Diseases and Functional Genomics Group, Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia
- Neurogenetics Laboratory, Department of Diagnostic Genomics, PP Block, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Igor Stevanovski
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Sydney, NSW 2010, Australia
| | - Sanjog R Chintalaphani
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2050, Australia
| | - Hasindu Gamaarachchi
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Sydney, NSW 2010, Australia
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW 2052, Australia
| | - Roula Ghaoui
- Department of Neurology, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA 5000, Australia
| | - Darshan Ghia
- UWA Medical School, University of Western Australia, Perth, WA 6009, Australia
- Neurology and Stroke Unit, Fiona Stanley Hospital, Murdoch, WA 6150, Australia
| | - Robert D Henderson
- Centre for Clinical Research, University of Queensland, Herston, QLD 4006, Australia
| | - Nerissa Jordan
- Department of Neurology, Fiona Stanley Hospital, Perth, WA 6150, Australia
| | - Antony Winkel
- Department of Neurosciences, Griffith University, Sunshine Coast University Hospital, Mount Gravatt, QLD 4111, Australia
| | | | | | - Richard H Roxburgh
- Centre for Brain Research Neurogenetics Research Clinic, University of Auckland, Auckland, New Zealand
| | - Ben Weisburd
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nigel G Laing
- Preventive Genetics Group, Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Ira W Deveson
- Genomics Pillar, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children’s Research Institute, Sydney, NSW 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW 2050, Australia
| | - Mark R Davis
- Neurogenetics Laboratory, Department of Diagnostic Genomics, PP Block, QEII Medical Centre, Nedlands, WA 6009, Australia
| | - Gianina Ravenscroft
- Rare Genetic Diseases and Functional Genomics Group, Centre for Medical Research, University of Western Australia, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, WA 6009, Australia
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4
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Folland C, Ganesh V, Weisburd B, McLean C, Kornberg AJ, O'Donnell-Luria A, Rehm HL, Stevanovski I, Chintalaphani SR, Kennedy P, Deveson IW, Ravenscroft G. Transcriptome and Genome Analysis Uncovers a DMD Structural Variant: A Case Report. Neurol Genet 2023; 9:e200064. [PMID: 37090938 PMCID: PMC10117699 DOI: 10.1212/nxg.0000000000200064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 01/27/2023] [Indexed: 03/16/2023]
Abstract
Objective Duchenne muscular dystrophy (DMD) is caused by pathogenic variants in the dystrophin gene (DMD). Hypermethylated CGG expansions within DIP2B 5' UTR are associated with an intellectual development disorder. Here, we demonstrate the diagnostic utility of genomic short-read sequencing (SRS) and transcriptome sequencing to identify a novel DMD structural variant (SV) and a DIP2B CGG expansion in a patient with DMD for whom conventional diagnostic testing failed to yield a genetic diagnosis. Methods We performed genomic SRS, skeletal muscle transcriptome sequencing, and targeted programmable long-read sequencing (LRS). Results The proband had a typical DMD clinical presentation, autism spectrum disorder (ASD), and dystrophinopathy on muscle biopsy. Transcriptome analysis identified 6 aberrantly expressed genes; DMD and DIP2B were the strongest underexpression and overexpression outliers, respectively. Genomic SRS identified a 216 kb paracentric inversion (NC_000023.11: g.33162217-33378800) overlapping 2 DMD promoters. ExpansionHunter indicated an expansion of 109 CGG repeats within the 5' UTR of DIP2B. Targeted genomic LRS confirmed the SV and genotyped the DIP2B repeat expansion as 270 CGG repeats. Discussion Here, transcriptome data heavily guided genomic analysis to resolve a complex DMD inversion and a DIP2B repeat expansion. Longitudinal follow-up will be important for clarifying the clinical significance of the DIP2B genotype.
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Affiliation(s)
- Chiara Folland
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Vijay Ganesh
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Ben Weisburd
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Catriona McLean
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Andrew J Kornberg
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Anne O'Donnell-Luria
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Heidi L Rehm
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Igor Stevanovski
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Sanjog R Chintalaphani
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Paul Kennedy
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Ira W Deveson
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
| | - Gianina Ravenscroft
- Centre for Medical Research, University of Western Australia (C.F., G.R.), Harry Perkins Institute of Medical Research, Perth, Australia; Center for Mendelian Genomics (V.G., B.W., A.O.-L., H.L.R.), Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA; Department of Neurology (V.G.), Brigham and Women's Hospital; Division of Genetics and Genomics (V.G., A.O.-L.), Boston Children's Hospital, MA; Department of Anatomical Pathology (C.M., P.K.), Alfred Health; Department of Medicine (C.M., P.K.), Central Clinical School, Monash University, Melbourne; Murdoch Children's Research Institute (A.J.K.); Department of Neurology (A.J.K.), Royal Children's Hospital; Department of Paediatrics (A.J.K.), University of Melbourne, Victoria, Australia; Center for Genomic Medicine (A.O.-L., H.L.R.), Massachusetts General Hospital, Boston, MA; Genomics Pillar (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research, Sydney, Australia; Centre for Population Genomics (I.S., S.R.C., I.W.D.), Garvan Institute of Medical Research and Murdoch Children's Research Institute, Australia; School of Clinical Medicine (S.R.C., I.W.D.), Faculty of Medicine and Health, UNSW Sydney, Australia; and School of Biomedical Sciences (G.R.), University of Western Australia, Perth, Australia
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5
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Stevanovski I, Chintalaphani SR, Gamaarachchi H, Ferguson JM, Pineda SS, Scriba CK, Tchan M, Fung V, Ng K, Cortese A, Houlden H, Dobson-Stone C, Fitzpatrick L, Halliday G, Ravenscroft G, Davis MR, Laing NG, Fellner A, Kennerson M, Kumar KR, Deveson IW. Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing. Sci Adv 2022; 8:eabm5386. [PMID: 35245110 PMCID: PMC8896783 DOI: 10.1126/sciadv.abm5386] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/11/2022] [Indexed: 05/25/2023]
Abstract
More than 50 neurological and neuromuscular diseases are caused by short tandem repeat (STR) expansions, with 37 different genes implicated to date. We describe the use of programmable targeted long-read sequencing with Oxford Nanopore's ReadUntil function for parallel genotyping of all known neuropathogenic STRs in a single assay. Our approach enables accurate, haplotype-resolved assembly and DNA methylation profiling of STR sites, from a list of predetermined candidates. This correctly diagnoses all individuals in a small cohort (n = 37) including patients with various neurogenetic diseases (n = 25). Targeted long-read sequencing solves large and complex STR expansions that confound established molecular tests and short-read sequencing and identifies noncanonical STR motif conformations and internal sequence interruptions. We observe a diversity of STR alleles of known and unknown pathogenicity, suggesting that long-read sequencing will redefine the genetic landscape of repeat disorders. Last, we show how the inclusion of pharmacogenomic genes as secondary ReadUntil targets can further inform patient care.
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Affiliation(s)
- Igor Stevanovski
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Sanjog R. Chintalaphani
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Medicine, University of New South Wales, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Hasindu Gamaarachchi
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- School of Computer Science and Engineering, University of New South Wales, Sydney, NSW, Australia
| | - James M. Ferguson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Sandy S. Pineda
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- The University of Sydney, Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, Camperdown, NSW, Australia
| | - Carolin K. Scriba
- Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA, Australia
- Diagnostic Genomics, PathWest Laboratory Medicine WA, Nedlands, WA, Australia
| | - Michel Tchan
- Westmead Hospital, Westmead, NSW, Australia and Sydney Medical School, The University of Sydney, NSW, Australia
| | - Victor Fung
- Westmead Hospital, Westmead, NSW, Australia and Sydney Medical School, The University of Sydney, NSW, Australia
| | - Karl Ng
- Department of Neurology, Royal North Shore Hospital and The University of Sydney, Sydney, NSW, Australia
| | - Andrea Cortese
- Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- The National Hospital for Neurology and Neurosurgery, London, UK
| | - Henry Houlden
- Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- The National Hospital for Neurology and Neurosurgery, London, UK
| | - Carol Dobson-Stone
- The University of Sydney, Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, Camperdown, NSW, Australia
| | - Lauren Fitzpatrick
- The University of Sydney, Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, Camperdown, NSW, Australia
| | - Glenda Halliday
- The University of Sydney, Brain and Mind Centre and School of Medical Sciences, Faculty of Medicine and Health, Camperdown, NSW, Australia
| | - Gianina Ravenscroft
- Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA, Australia
| | - Mark R. Davis
- Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA, Australia
| | - Nigel G. Laing
- Harry Perkins Institute of Medical Research, University of Western Australia, Nedlands, WA, Australia
- Diagnostic Genomics, PathWest Laboratory Medicine WA, Nedlands, WA, Australia
| | - Avi Fellner
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Raphael Recanati Genetics Institute, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
- The Neurology Department, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel
| | - Marina Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, NSW, Australia
- Faculty of Health and Medicine, University of Sydney, Camperdown, NSW, Australia
- Molecular Medicine Laboratory, Concord Hospital, Concord, NSW, Australia
| | - Kishore R. Kumar
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Molecular Medicine Laboratory, Concord Hospital, Concord, NSW, Australia
- Neurology Department, Central Clinical School, Concord Repatriation General Hospital, University of Sydney, Concord, NSW, Australia
| | - Ira W. Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
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6
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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: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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