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Rafehi H, Fearnley LG, Read J, Snell P, Davies KC, Scott L, Gillies G, Thompson GC, Field TA, Eldo A, Bodek S, Butler E, Chen L, Drago J, Goel H, Hackett A, Halmagyi GM, Hannaford A, Kotschet K, Kumar KR, Kumble S, Lee-Archer M, Malhotra A, Paine M, Poon M, Pope K, Reardon K, Ring S, Ronan A, Silsby M, Smyth R, Stutterd C, Wallis M, Waterston J, Wellings T, West K, Wools C, Wu KHC, Szmulewicz DJ, Delatycki MB, Bahlo M, Lockhart PJ. A prospective trial comparing programmable targeted long-read sequencing and short-read genome sequencing for genetic diagnosis of cerebellar ataxia. Genome Res 2025; 35:769-785. [PMID: 40015980 PMCID: PMC12047251 DOI: 10.1101/gr.279634.124] [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: 06/11/2024] [Accepted: 11/21/2024] [Indexed: 03/01/2025]
Abstract
The cerebellar ataxias (CAs) are a heterogeneous group of disorders characterized by progressive incoordination. Seventeen repeat expansion (RE) loci have been identified as the primary genetic cause and account for >80% of genetic diagnoses. Despite this, diagnostic testing is limited and inefficient, often utilizing single gene assays. This study evaluates the effectiveness of long- and short-read sequencing as diagnostic tools for CA. We recruited 110 individuals (48 females, 62 males) with a clinical diagnosis of CA. Short-read genome sequencing (SR-GS) was performed to identify pathogenic RE and also non-RE variants in 356 genes associated with CA. Independently, long-read sequencing with adaptive sampling (LR-AS) was performed to identify pathogenic RE. SR-GS provided a genetic diagnosis for 38% of the cohort (40/110) including seven non-RE pathogenic variants. RE causes disease in 33 individuals, with the most common condition being SCA27B (n = 24). In comparison, LR-AS identified pathogenic RE in 29 individuals. RE identification for the two methods was concordant apart from four SCA27B cases not detected by LR-AS due to low read depth. For both technologies manual review of the RE alignment enhances diagnostic outcomes. Orthogonal testing for SCA27B revealed a 15% and 0% false positive rate for SR-GS and LR-AS, respectively. In conclusion, both technologies are powerful screening tools for CA. SR-GS is a mature technology currently used by diagnostic providers, requiring only minor changes in bioinformatic workflows to enable CA diagnostics. LR-AS offers considerable advantages in the context of RE detection and characterization but requires optimization before clinical implementation.
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Affiliation(s)
- Haloom Rafehi
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Liam G Fearnley
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Justin Read
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
- Department of Neuroscience, Central Clinical School, Monash University, The Alfred Centre, Melbourne, Victoria 3004, Australia
| | - Penny Snell
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - Kayli C Davies
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - Liam Scott
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Greta Gillies
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - Genevieve C Thompson
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - Tess A Field
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - Aleena Eldo
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - Simon Bodek
- Austin Health, Heidelberg, Victoria 3084, Australia
| | - Ernest Butler
- Monash Medical Centre, Clayton, Victoria 3168, Australia
| | - Luke Chen
- Department of Neurology, Alfred Hospital, Melbourne, Victoria 3004, Australia
| | - John Drago
- Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, Victoria 3065, Australia
- Florey Institute of Neuroscience and Mental Health, Parkville, Victoria 3052, Australia
| | - Himanshu Goel
- Hunter Genetics, Hunter New England Health Service, Waratah, New South Wales 2298, Australia
| | - Anna Hackett
- Hunter Genetics, Hunter New England Health Service, Waratah, New South Wales 2298, Australia
- University of Newcastle, Callaghan, New South Wales 2308, Australia
| | - G Michael Halmagyi
- Neurology Department, Royal Prince Alfred Hospital, Camperdown, New South Wales 2050, Australia
- Central Clinical School, University of Sydney, Camperdown, New South Wales 2050, Australia
| | - Andrew Hannaford
- Department of Neurology, Westmead Hospital, Hawkesbury Westmead, New South Wales 2145, Australia
- Brain and Nerve Research Centre, Concord Clinical School, University of Sydney, Camperdown, New South Wales 2050, Australia
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia
| | - Katya Kotschet
- Department of Clinical Neurosciences, St Vincent's Hospital, University of Melbourne, Fitzroy, Victoria 3065, Australia
| | - Kishore R Kumar
- Molecular Medicine Laboratory and Neurology Department, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia
- Faculty of Medicine and Health, The University of Sydney, Camperdown, New South Wales 2050, Australia
- Genomics and Inherited Disease Program, The Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
- School of Medicine, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Smitha Kumble
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
- Department of Clinical Genetics, Austin Health, Viewbank, Victoria 3084, Australia
| | - Matthew Lee-Archer
- Department of Neurology, Launceston General Hospital, Launceston, Tasmania 7250, Australia
| | - Abhishek Malhotra
- Department of Neuroscience, University Hospital Geelong, Geelong, Victoria 3220, Australia
| | - Mark Paine
- Department of Neurology, Royal Brisbane and Women's Hospital, Herston, Queensland 4006, Australia
| | - Michael Poon
- Neurology Footscray, Footscray, Victoria 3011, Australia
| | - Kate Pope
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - Katrina Reardon
- Department of Medicine, St Vincent's Hospital, University of Melbourne, Fitzroy, Victoria 3065, Australia
- Department of Neurology, St Vincent's Hospital, University of Melbourne, Fitzroy, Victoria 3065, Australia
| | - Steven Ring
- Albury Wodonga Health, West Albury, New South Wales 2640, Australia
| | - Anne Ronan
- University of Newcastle, Callaghan, New South Wales 2308, Australia
- Newcastle Medical Genetics, Lambton, New South Wales 2299, Australia
| | - Matthew Silsby
- Department of Neurology, Westmead Hospital, Hawkesbury Westmead, New South Wales 2145, Australia
- Brain and Nerve Research Centre, Concord Clinical School, University of Sydney, Camperdown, New South Wales 2050, Australia
- Department of Neurology, Concord Repatriation General Hospital, Concord, New South Wales 2139, Australia
| | - Renee Smyth
- St Vincent's Clinical Genomics, St Vincent's Hospital, Darlinghurst, New South Wales 2010, Australia
| | - Chloe Stutterd
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - Mathew Wallis
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, Royal Hobart Hospital, Hobart, Tasmania 7001, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - John Waterston
- Department of Neuroscience, Central Clinical School, Monash University, The Alfred Centre, Melbourne, Victoria 3004, Australia
| | - Thomas Wellings
- Department of Neurology, John Hunter Hospital, New Lambton Heights, New South Wales 2305, Australia
| | - Kirsty West
- Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria 3052, Australia
| | - Christine Wools
- Department of Neurology, Calvary Health Care Bethlehem, Caulfield South Victoria 3162, Australia
- Department of Neurology, The Royal Melbourne Hospital, Parkville, Victoria 3052, Australia
| | - Kathy H C Wu
- St Vincent's Clinical Genomics, St Vincent's Hospital, Darlinghurst, New South Wales 2010, Australia
- School of Medicine, University of Notre Dame, Darlinghurst, New South Wales 2010, Australia
- Discipline of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Camperdown, New South Wales 2050, Australia
| | - David J Szmulewicz
- Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria 3002, Australia
- Bionics Institute, East Melbourne, Victoria 3002, Australia
| | - Martin B Delatycki
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria 3052, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Paul J Lockhart
- Bruce Lefroy Centre, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria 3052, Australia;
- Department of Paediatrics, University of Melbourne, Royal Children's Hospital, Parkville, Victoria 3052, Australia
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Miura S, Shimojo T, Morikawa T, Kamada T, Uchiyama Y, Kurata S, Fujioka R, Shibata H. Familial paroxysmal kinesigenic dyskinesia with a novel missense variant (Arg2866Trp) in NBEA. J Hum Genet 2021; 66:805-811. [PMID: 33692494 DOI: 10.1038/s10038-021-00914-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 11/10/2022]
Abstract
Paroxysmal kinesigenic dyskinesia (PKD) is a movement disorder characterized by episodic involuntary movement attacks triggered by sudden movements, acceleration, or intention to move. We ascertained two Japanese familial cases with PKD. The proband is a 22-year-old woman who had noted sudden brief (<30 s) of involuntary movements provoked by kinesigenic trigger such as starting to run, getting on a train, picking up a telephone receiver and so on at the age of 14. Interictal brain single photon emission computed tomography (SPECT) showed hyperperfusion in the left thalamus. A 46-year-old woman, the mother of the proband was also suffering from brief attacks triggered by starting to run in her high school days. On neurological examination, both showed no abnormality. Whole exome sequencing combined with rigorous filtering revealed two heterozygous nonsynonymous variants (NM_001447: c.8976G > C [p.Gln2992His] in FAT2 and NM_015678: c.8596C > T [p.Arg2866Trp] in NBEA). Real time quantitative PCR analysis of Nbea mRNA levels in the developing rat brain revealed peak at postnatal day 28 and decline at postnatal day 56. This result might match the most common clinical course of PKD from the point of view of the most common age at remission. NBEA has been reported to be responsible for neurodevelopmental disease accompanied by epilepsy. We concluded the variant in NBEA most likely to be responsible for our familial cases of PKD.
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Affiliation(s)
- Shiroh Miura
- Department of Neurology and Geriatric Medicine, Ehime University Graduate School of Medicine, Toon, 791-0295, Japan.,Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Tomofumi Shimojo
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Takuya Morikawa
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Takashi Kamada
- Department of Neurology, Fukuoka Sanno Hospital, Fukuoka, 814-0001, Japan
| | - Yusuke Uchiyama
- Department of Radiology, Kurume University School of Medicine, Kurume, 830-0011, Japan
| | - Seiji Kurata
- Department of Radiology, Kurume University School of Medicine, Kurume, 830-0011, Japan
| | - Ryuta Fujioka
- Department of Food and Nutrition, Beppu University Junior College, Beppu, 874-8501, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
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