Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants.

Autor:	Bournazos AM; Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia., Riley LG; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Rare Diseases Functional Genomics, Kids Research, Sydney Children's Hospital Network and Children's Medical Research Institute, Westmead, New South Wales, Australia., Bommireddipalli S; Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia., Ades L; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia., Akesson LS; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; Department of Pathology, University of Melbourne, Parkville, Victoria, Australia; Department of Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia; Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia., Al-Shinnag M; Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia; The University of Queensland, Herston, Queensland, Australia., Alexander SI; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Westmead, New South Wales, Australia., Archibald AD; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia., Balasubramaniam S; Genetic Metabolic Disorders Service, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Western Sydney Genetics Program, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia., Berman Y; Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, New South Wales, Australia; Northern Clinical School, Royal North Shore Hospital, St Leonards, New South Wales, Australia., Beshay V; Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia., Boggs K; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Australian Genomics Health Alliance, Parkville, Victoria, Australia; Centre for Clinical Genetics, Sydney Children's Hospital Randwick, Randwick, New South Wales, Australia., Bojadzieva J; Department of Clinical Genetics, Austin Health, Heidelberg, Victoria, Australia., Brown NJ; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia., Bryen SJ; Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia., Buckley MF; NSW Health Pathology, Randwick, New South Wales, Australia., Chong B; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia., Davis MR; Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia., Dawes R; Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia., Delatycki M; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia., Donaldson L; The Royal Melbourne Hospital, Parkville, Victoria, Australia., Downie L; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; The Royal Melbourne Hospital, Parkville, Victoria, Australia; Murdoch Children's Research Institute, Parkville, Victoria, Australia., Edwards C; Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia., Edwards M; Department of Paediatrics, School of Medicine, Western Sydney University, Penrith South, New South Wales, Australia., Engel A; ACT Genetic Service, ACT Health, The Canberra Hospital, Garran, ACT, Australia., Ewans LJ; Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia; Central Clinical School, The University of Sydney, Camperdown, New South Wales, Australia., Faiz F; Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia., Fennell A; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Monash Genetics, Monash Health, Clayton, Victoria, Australia., Field M; Genetics of Learning Disability Service, Hunter Genetics, Waratah, New South Wales, Australia., Freckmann ML; Department of Clinical Genetics, The Canberra Hospital, Garran, ACT, Australia., Gallacher L; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia., Gear R; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia., Goel H; Genetics of Learning Disability Service, Hunter Genetics, Waratah, New South Wales, Australia; The University of Newcastle, Callaghan, New South Wales, Australia., Goh S; Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia., Goodwin L; Department of Clinical Genetics, Nepean Hospital, Kingswood, New South Wales, Australia., Hanna B; Department of Genomic Medicine, Westmead Hospital, Westmead, New South Wales, Australia., Harraway J; Sullivan Nicolaides Pathology, Bowen Hills, Queensland, Australia., Higgins M; Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia., Ho G; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia., Hopper BK; Forster Genetics, Forster, New South Wales, Australia., Horton AE; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Monash Genetics, Monash Health, Clayton, Victoria, Australia; Monash Heart and Monash Children's Hospital, Monash Health, Clayton, Victoria, Australia; Monash Cardiovascular Research Centre, Clayton, Victoria, Australia., Hunter MF; Monash Genetics, Monash Health, Clayton, Victoria, Australia; Department of Paediatrics, Monash University, Clayton, Victoria, Australia., Huq AJ; Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; The Royal Melbourne Hospital, Parkville, Victoria, Australia., Josephi-Taylor S; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Genomic Medicine, Westmead Hospital, Westmead, New South Wales, Australia., Joshi H; Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia., Kirk E; NSW Health Pathology, Randwick, New South Wales, Australia; Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia., Krzesinski E; Monash Genetics, Monash Health, Clayton, Victoria, Australia; Department of Paediatrics, Monash University, Clayton, Victoria, Australia., Kumar KR; Department of Neurogenetics, Kolling Institute, Faculty of Medicine and Health, University of Sydney, Royal North Shore Hospital, St Leonards, New South Wales, Australia; Translational Genomics, Kinghorn Centre for Clinical Genomics, Garvan Institute for Medical Research, Darlinghurst, New South Wales, Australia., Lemckert F; Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia., Leventer RJ; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Murdoch Children's Research Institute, Parkville, Victoria, Australia; Department of Neurology, The Royal Children's Hospital, Parkville, Victoria, Australia., Lindsey-Temple SE; Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Kensington, NSW, Australia., Lunke S; Department of Pathology, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia., Ma A; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia., Macaskill S; Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia., Mallawaarachchi A; Department of Medical Genomics, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia; Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia., Marty M; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia., Marum JE; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia., McCarthy HJ; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Pediatric Nephrology, The Children's Hospital at Westmead, Westmead, New South Wales, Australia., Menezes MP; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; The TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, New South Wales, Australia., McLean A; Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia., Milnes D; Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia., Mohammad S; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; The TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, New South Wales, Australia., Mowat D; Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Kensington, NSW, Australia., Niaz A; Rare Diseases Functional Genomics, Kids Research, Sydney Children's Hospital Network and Children's Medical Research Institute, Westmead, New South Wales, Australia., Palmer EE; Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Kensington, NSW, Australia., Patel C; Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia., Patel SG; School of Medicine, The University of Auckland, Auckland, New Zealand., Phelan D; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia., Pinner JR; Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Kensington, NSW, Australia., Rajagopalan S; Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia., Regan M; Monash Genetics, Monash Health, Clayton, Victoria, Australia; Department of Paediatrics, Monash University, Clayton, Victoria, Australia., Rodgers J; Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia., Rodrigues M; Department of Neurology, Auckland City Hospital, Auckland, New Zealand., Roxburgh RH; Department of Neurology, Auckland City Hospital, Auckland, New Zealand., Sachdev R; Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia., Roscioli T; NSW Health Pathology, Randwick, New South Wales, Australia; Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia; Neuroscience Research Australia, University of New South Wales, Randwick, New South Wales, Australia., Samarasekera R; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia., Sandaradura SA; Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia., Savva E; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia., Schindler T; School of Women's and Children's Health, Faculty of Medicine and Health, University of New South Wales, Kensington, NSW, Australia; Newborn Care, Royal Hospital for Women, Randwick, New South Wales, Australia., Shah M; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia., Sinnerbrink IB; Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Clinical Genetics, Nepean Hospital, Kingswood, New South Wales, Australia., Smith JM; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia., Smith RJ; Molecular Otolaryngology and Renal Research Laboratories, Carver College of Medicine, University of Iowa, Iowa City, IA, United States., Springer A; Department of Paediatrics, Monash University, Clayton, Victoria, Australia., Stark Z; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia., Strom SP; Fulgent Genetics, Temple City, CA., Sue CM; Department of Neurogenetics, Kolling Institute, Faculty of Medicine and Health, University of Sydney, Royal North Shore Hospital, St Leonards, New South Wales, Australia., Tan K; Department of Paediatrics, Monash University, Clayton, Victoria, Australia; Monash Newborn, Monash Children's Hospital, Clayton, Victoria, Australia., Tan TY; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia., Tantsis E; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; The TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, New South Wales, Australia., Tchan MC; Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Genomic Medicine, Westmead Hospital, Westmead, New South Wales, Australia., Thompson BA; Department of Pathology, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia., Trainer AH; Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; Department of Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia., van Spaendonck-Zwarts K; Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia., Walsh R; NSW Health Pathology, Randwick, New South Wales, Australia., Warwick L; ACT Genetic Service, ACT Health, The Canberra Hospital, Garran, ACT, Australia., White S; Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, New South Wales, Australia., White SM; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia., Williams MG; Mater Research Institute, The University of Queensland, South Brisbane, Queensland, Australia., Wilson MJ; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia., Wong WK; Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; The TY Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Westmead, New South Wales, Australia., Wright DC; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Specialty of Genomic Medicine, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Cytogenetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia., Yap P; Northern Hub, Genetic Health Service NZ, Auckland, New Zealand., Yeung A; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia., Young H; Department of Intensive Care, Austin Hospital, Heidelberg, Victoria, Australia., Jones KJ; Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia., Bennetts B; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; Department of Molecular Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia., Cooper ST; Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia; Department of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia; The Children's Medical Research Institute, Westmead, New South Wales, Australia. Electronic address: sandra.cooper@sydney.edu.au.
Jazyk:	angličtina
Zdroj:	Genetics in medicine : official journal of the American College of Medical Genetics [Genet Med] 2022 Jan; Vol. 24 (1), pp. 130-145. Date of Electronic Publication: 2021 Nov 30.
DOI:	10.1016/j.gim.2021.09.001
Abstrakt:	Purpose: Genetic variants causing aberrant premessenger RNA splicing are increasingly being recognized as causal variants in genetic disorders. In this study, we devise standardized practices for polymerase chain reaction (PCR)-based RNA diagnostics using clinically accessible specimens (blood, fibroblasts, urothelia, biopsy). Methods: A total of 74 families with diverse monogenic conditions (31% prenatal-congenital onset, 47% early childhood, and 22% teenage-adult onset) were triaged into PCR-based RNA testing, with comparative RNA sequencing for 19 cases. Results: Informative RNA assay data were obtained for 96% of cases, enabling variant reclassification for 75% variants that can be used for genetic counseling (71%), to inform clinical care (32%) and prenatal counseling (41%). Variant-associated mis-splicing was highly reproducible for 28 cases with samples from ≥2 affected individuals or heterozygotes and 10 cases with ≥2 biospecimens. PCR amplicons encompassing another segregated heterozygous variant was vital for clinical interpretation of 22 of 79 variants to phase RNA splicing events and discern complete from partial mis-splicing. Conclusion: RNA diagnostics enabled provision of a genetic diagnosis for 64% of recruited cases. PCR-based RNA diagnostics has capacity to analyze 81.3% of clinically significant genes, with long amplicons providing an advantage over RNA sequencing to phase RNA splicing events. The Australasian Consortium for RNA Diagnostics (SpliceACORD) provide clinically-endorsed, standardized protocols and recommendations for interpreting RNA assay data. Competing Interests: Conflict of Interest Sandra T. Cooper is director of Frontier Genomics Pty Ltd (Australia). Sandra T. Cooper currently receives no consultancy fees or other remuneration for this role. Frontier Genomics Pty Ltd (Australia) has no existing financial relationships that will benefit from publication of these data. Samuel P. Strom is an employee and shareholder of Fulgent Genetics. Michael F. Buckley is an employee and shareholder of Invitae. The remaining coauthors declare no conflicts of interest. (Copyright © 2021. Published by Elsevier Inc.)
Databáze:	MEDLINE
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