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

doi:10.1016/j.gim.2021.09.001

. 2022 Jan;24(1):130-145.

doi: 10.1016/j.gim.2021.09.001. Epub 2021 Nov 30.

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

Adam M Bournazos¹, Lisa G Riley², Shobhana Bommireddipalli³, Lesley Ades⁴, Lauren S Akesson⁵, Mohammad Al-Shinnag⁶, Stephen I Alexander⁷, Alison D Archibald⁸, Shanti Balasubramaniam⁹, Yemima Berman¹⁰, Victoria Beshay¹¹, Kirsten Boggs¹², Jasmina Bojadzieva¹³, Natasha J Brown⁸, Samantha J Bryen¹, Michael F Buckley¹⁴, Belinda Chong¹⁵, Mark R Davis¹⁶, Ruebena Dawes¹, Martin Delatycki⁸, Liz Donaldson¹⁷, Lilian Downie¹⁸, Caitlin Edwards¹⁶, Matthew Edwards¹⁹, Amanda Engel²⁰, Lisa J Ewans²¹, Fathimath Faiz¹⁶, Andrew Fennell²², Michael Field²³, Mary-Louise Freckmann²⁴, Lyndon Gallacher⁸, Russell Gear¹⁵, Himanshu Goel²⁵, Shuxiang Goh²⁶, Linda Goodwin²⁷, Bernadette Hanna²⁸, James Harraway²⁹, Megan Higgins³⁰, Gladys Ho³¹, Bruce K Hopper³², Ari E Horton³³, Matthew F Hunter³⁴, Aamira J Huq³⁵, Sarah Josephi-Taylor³⁶, Himanshu Joshi³, Edwin Kirk³⁷, Emma Krzesinski³⁴, Kishore R Kumar³⁸, Frances Lemckert¹, Richard J Leventer³⁹, Suzanna E Lindsey-Temple⁴⁰, Sebastian Lunke⁴¹, Alan Ma⁴, Steven Macaskill¹¹, Amali Mallawaarachchi⁴², Melanie Marty¹⁵, Justine E Marum¹⁵, Hugh J McCarthy⁷, Manoj P Menezes⁴³, Alison McLean²⁶, Di Milnes³⁰, Shekeeb Mohammad⁴³, David Mowat⁴⁴, Aram Niaz⁴⁵, Elizabeth E Palmer⁴⁴, Chirag Patel³⁰, Shilpan G Patel⁴⁶, Dean Phelan¹⁵, Jason R Pinner⁴⁴, Sulekha Rajagopalan²⁶, Matthew Regan³⁴, Jonathan Rodgers³⁰, Miriam Rodrigues⁴⁷, Richard H Roxburgh⁴⁷, Rani Sachdev⁴⁸, Tony Roscioli⁴⁹, Ruvishani Samarasekera⁵⁰, Sarah A Sandaradura⁵¹, Elena Savva¹⁵, Tim Schindler⁵², Margit Shah⁵⁰, Ingrid B Sinnerbrink⁵³, Janine M Smith⁵⁴, Richard J Smith⁵⁵, Amanda Springer⁵⁶, Zornitza Stark⁸, Samuel P Strom⁵⁷, Carolyn M Sue⁵⁸, Kenneth Tan⁵⁹, Tiong Y Tan⁸, Esther Tantsis⁴³, Michel C Tchan⁶⁰, Bryony A Thompson⁶¹, Alison H Trainer⁶², Karin van Spaendonck-Zwarts³⁰, Rebecca Walsh¹⁴, Linda Warwick²⁰, Stephanie White⁶³, Susan M White⁸, Mark G Williams⁶⁴, Meredith J Wilson⁵⁴, Wui Kwan Wong⁶⁵, Dale C Wright⁶⁶, Patrick Yap⁶⁷, Alison Yeung⁸, Helen Young⁶⁸, Kristi J Jones⁵¹, Bruce Bennetts³¹, Sandra T Cooper⁶⁹; Australasian Consortium for RNA Diagnostics

Collaborators, Affiliations

Collaborators

Australasian Consortium for RNA Diagnostics:
Ghusoon Abdulrasool, Lauren S Akesson, Ghamdan Al Eryani, Mohammad Al-Shinnag, Peer Arts, Richard Bagnall, Naomi L Baker, Christopher Barnett, Sarah Beecroft, Bruce Bennetts, Marina Berbic, Victoria Beshay, Michael Black, Jim Blackburn, Piers Blombery, Kirsten Boggs, Adam M Bournazos, Susan Branford, Jimmy Breen, Natasha J Brown, Samantha J Bryen, Leslie Burnett, Daffodil Canson, Pak Cheong, Edward Chew, Belinda Chong, John Christodoulou, Seo-Kyung Chung, Mike Clark, Corrina Cliffe, Melissa Cole, Felicity Collins, Alison Compton, Antony Cooper, Sandra T Cooper, Mark Corbett, Mark Cowley, Mark R Davis, Martin Delatycki, Tracy Dudding, Matthew Edwards, Stefanie Eggers, Lisa J Ewans, Eduardo Eyras, Fathimath Faiz, Miriam Fanjul Fernandez, Andrew Fellowes, Andrew Fennell, Michael Field, Ron Fleischer, Chiara Folland, Lucy Fox, Mary-Louise Freckmann, Clara Gaff, Melanie Galea, Roula Ghaoui, Himanshu Goel, Ilias Gornanitis, Thuong Ha, Bernadette Hanna, James Harraway, Rippei Hayashi, Ian Hayes, Alex Henderson, Luke Hesson, Erin Heyer, Michael Hildebrand, Michael Hipwell, Gladys Ho, Ari E Horton, Cass Hoskins, Matthew F Hunter, Matilda Jackson, Paul James, Kristi J Jones, Justin Jong-Leong Wong, Sarah Josephi-Taylor, Himanshu Joshi, Karin Kassahn, Peter Kaub, Lucy Kevin, Edwin Kirk, Emma Krzesinski, Smitha Kumble, Sarah Kummerfeld, Nigel Laing, Chiyan Lau, Eric Lee, Sarah Leighton, Ben Lundie, Sebastian Lunke, Amali Mallawaarachchi, Chelsea Mayoh, Julie McGaughran, Alison McLean, Mary McPhillips, Cliff Meldrum, Edwina Middleton, Di Milnes, Kym Mina, David Mowat, Amy Nisselle, Emily Oates, Alicia Oshlack, Elizabeth E Palmer, Gayathri Parasivam, Michael Parsons, Chirag Patel, Jason R Pinner, Michael Quinn, John Rasko, Gina Ravenscroft, Anja Ravine, Krista Recsei, Matthew Regan, Jacqueline Rehn, Lisa G Riley, Stephen Robertson, Anne Ronan, Tony Roscioli, Georgina Ryland, Simon Sadedin, Sarah A Sandaradura, Andreas Schreiber, Hamish Scott, Rodney Scott, Christopher Semsarian, Cas Simons, Emma Singer, Janine M Smith, Renee Smyth, Amanda Spurdle, Zornitza Stark, Patricia Sullivan, Samantha Sundercombe, Tiong Y Tan, Michel C Tchan, Bryony A Thompson, David Thorburn, John Toubia, Ronald Trent, Emma Tudini, Irina Voneague, Leigh Waddell, Logan Walker, Mathew Wallis, Nick Warnock, Robert Weatheritt, Deborah White, Susan M White, Mark G Williams, Meredith J Wilson, Ingrid Winship, Lisa Worgan, Dale C Wright, Kathy Wu, Alison Yeung, Andrew Ziolowski

Affiliations

¹ 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.
² 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.
³ Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia.
⁴ 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.
⁵ 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.
⁶ Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia; The University of Queensland, Herston, Queensland, Australia.
⁷ 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.
⁸ Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia.
⁹ 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.
¹⁰ 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.
¹¹ Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
¹² 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.
¹³ Department of Clinical Genetics, Austin Health, Heidelberg, Victoria, Australia.
¹⁴ NSW Health Pathology, Randwick, New South Wales, Australia.
¹⁵ Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia.
¹⁶ Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia.
¹⁷ The Royal Melbourne Hospital, Parkville, Victoria, Australia.
¹⁸ Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; The Royal Melbourne Hospital, Parkville, Victoria, Australia; Murdoch Children's Research Institute, Parkville, Victoria, Australia.
¹⁹ Department of Paediatrics, School of Medicine, Western Sydney University, Penrith South, New South Wales, Australia.
²⁰ ACT Genetic Service, ACT Health, The Canberra Hospital, Garran, ACT, Australia.
²¹ 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.
²² Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Monash Genetics, Monash Health, Clayton, Victoria, Australia.
²³ Genetics of Learning Disability Service, Hunter Genetics, Waratah, New South Wales, Australia.
²⁴ Department of Clinical Genetics, The Canberra Hospital, Garran, ACT, Australia.
²⁵ Genetics of Learning Disability Service, Hunter Genetics, Waratah, New South Wales, Australia; The University of Newcastle, Callaghan, New South Wales, Australia.
²⁶ Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia.
²⁷ Department of Clinical Genetics, Nepean Hospital, Kingswood, New South Wales, Australia.
²⁸ Department of Genomic Medicine, Westmead Hospital, Westmead, New South Wales, Australia.
²⁹ Sullivan Nicolaides Pathology, Bowen Hills, Queensland, Australia.
³⁰ Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia.
³¹ 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.
³² Forster Genetics, Forster, New South Wales, Australia.
³³ 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.
³⁴ Monash Genetics, Monash Health, Clayton, Victoria, Australia; Department of Paediatrics, Monash University, Clayton, Victoria, Australia.
³⁵ Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; The Royal Melbourne Hospital, Parkville, Victoria, Australia.
³⁶ 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.
³⁷ NSW Health Pathology, Randwick, New South Wales, Australia; Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia.
³⁸ 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.
³⁹ 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.
⁴⁰ 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.
⁴¹ Department of Pathology, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia.
⁴² 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.
⁴³ 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.
⁴⁴ 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.
⁴⁵ Rare Diseases Functional Genomics, Kids Research, Sydney Children's Hospital Network and Children's Medical Research Institute, Westmead, New South Wales, Australia.
⁴⁶ School of Medicine, The University of Auckland, Auckland, New Zealand.
⁴⁷ Department of Neurology, Auckland City Hospital, Auckland, New Zealand.
⁴⁸ Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia.
⁴⁹ 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.
⁵⁰ Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia.
⁵¹ 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.
⁵² 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.
⁵³ 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.
⁵⁴ 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.
⁵⁵ Molecular Otolaryngology and Renal Research Laboratories, Carver College of Medicine, University of Iowa, Iowa City, IA, United States.
⁵⁶ Department of Paediatrics, Monash University, Clayton, Victoria, Australia.
⁵⁷ Fulgent Genetics, Temple City, CA.
⁵⁸ Department of Neurogenetics, Kolling Institute, Faculty of Medicine and Health, University of Sydney, Royal North Shore Hospital, St Leonards, New South Wales, Australia.
⁵⁹ Department of Paediatrics, Monash University, Clayton, Victoria, Australia; Monash Newborn, Monash Children's Hospital, Clayton, Victoria, Australia.
⁶⁰ 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.
⁶¹ Department of Pathology, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia.
⁶² Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; Department of Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia.
⁶³ Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, New South Wales, Australia.
⁶⁴ Mater Research Institute, The University of Queensland, South Brisbane, Queensland, Australia.
⁶⁵ 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.
⁶⁶ 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.
⁶⁷ Northern Hub, Genetic Health Service NZ, Auckland, New Zealand.
⁶⁸ Department of Intensive Care, Austin Hospital, Heidelberg, Victoria, Australia.
⁶⁹ 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.

PMID: 34906502
DOI: 10.1016/j.gim.2021.09.001

Free article

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

Adam M Bournazos et al. Genet Med. 2022 Jan.

Free article

. 2022 Jan;24(1):130-145.

doi: 10.1016/j.gim.2021.09.001. Epub 2021 Nov 30.

Authors

Collaborators

Australasian Consortium for RNA Diagnostics:
Ghusoon Abdulrasool, Lauren S Akesson, Ghamdan Al Eryani, Mohammad Al-Shinnag, Peer Arts, Richard Bagnall, Naomi L Baker, Christopher Barnett, Sarah Beecroft, Bruce Bennetts, Marina Berbic, Victoria Beshay, Michael Black, Jim Blackburn, Piers Blombery, Kirsten Boggs, Adam M Bournazos, Susan Branford, Jimmy Breen, Natasha J Brown, Samantha J Bryen, Leslie Burnett, Daffodil Canson, Pak Cheong, Edward Chew, Belinda Chong, John Christodoulou, Seo-Kyung Chung, Mike Clark, Corrina Cliffe, Melissa Cole, Felicity Collins, Alison Compton, Antony Cooper, Sandra T Cooper, Mark Corbett, Mark Cowley, Mark R Davis, Martin Delatycki, Tracy Dudding, Matthew Edwards, Stefanie Eggers, Lisa J Ewans, Eduardo Eyras, Fathimath Faiz, Miriam Fanjul Fernandez, Andrew Fellowes, Andrew Fennell, Michael Field, Ron Fleischer, Chiara Folland, Lucy Fox, Mary-Louise Freckmann, Clara Gaff, Melanie Galea, Roula Ghaoui, Himanshu Goel, Ilias Gornanitis, Thuong Ha, Bernadette Hanna, James Harraway, Rippei Hayashi, Ian Hayes, Alex Henderson, Luke Hesson, Erin Heyer, Michael Hildebrand, Michael Hipwell, Gladys Ho, Ari E Horton, Cass Hoskins, Matthew F Hunter, Matilda Jackson, Paul James, Kristi J Jones, Justin Jong-Leong Wong, Sarah Josephi-Taylor, Himanshu Joshi, Karin Kassahn, Peter Kaub, Lucy Kevin, Edwin Kirk, Emma Krzesinski, Smitha Kumble, Sarah Kummerfeld, Nigel Laing, Chiyan Lau, Eric Lee, Sarah Leighton, Ben Lundie, Sebastian Lunke, Amali Mallawaarachchi, Chelsea Mayoh, Julie McGaughran, Alison McLean, Mary McPhillips, Cliff Meldrum, Edwina Middleton, Di Milnes, Kym Mina, David Mowat, Amy Nisselle, Emily Oates, Alicia Oshlack, Elizabeth E Palmer, Gayathri Parasivam, Michael Parsons, Chirag Patel, Jason R Pinner, Michael Quinn, John Rasko, Gina Ravenscroft, Anja Ravine, Krista Recsei, Matthew Regan, Jacqueline Rehn, Lisa G Riley, Stephen Robertson, Anne Ronan, Tony Roscioli, Georgina Ryland, Simon Sadedin, Sarah A Sandaradura, Andreas Schreiber, Hamish Scott, Rodney Scott, Christopher Semsarian, Cas Simons, Emma Singer, Janine M Smith, Renee Smyth, Amanda Spurdle, Zornitza Stark, Patricia Sullivan, Samantha Sundercombe, Tiong Y Tan, Michel C Tchan, Bryony A Thompson, David Thorburn, John Toubia, Ronald Trent, Emma Tudini, Irina Voneague, Leigh Waddell, Logan Walker, Mathew Wallis, Nick Warnock, Robert Weatheritt, Deborah White, Susan M White, Mark G Williams, Meredith J Wilson, Ingrid Winship, Lisa Worgan, Dale C Wright, Kathy Wu, Alison Yeung, Andrew Ziolowski

Affiliations

¹ 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.
² 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.
³ Kids Neuroscience Centre, Kids Research, The Children's Hospital at Westmead, Westmead, New South Wales, Australia.
⁴ 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.
⁵ 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.
⁶ Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia; The University of Queensland, Herston, Queensland, Australia.
⁷ 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.
⁸ Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia.
⁹ 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.
¹⁰ 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.
¹¹ Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
¹² 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.
¹³ Department of Clinical Genetics, Austin Health, Heidelberg, Victoria, Australia.
¹⁴ NSW Health Pathology, Randwick, New South Wales, Australia.
¹⁵ Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia.
¹⁶ Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Western Australia, Australia.
¹⁷ The Royal Melbourne Hospital, Parkville, Victoria, Australia.
¹⁸ Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; The Royal Melbourne Hospital, Parkville, Victoria, Australia; Murdoch Children's Research Institute, Parkville, Victoria, Australia.
¹⁹ Department of Paediatrics, School of Medicine, Western Sydney University, Penrith South, New South Wales, Australia.
²⁰ ACT Genetic Service, ACT Health, The Canberra Hospital, Garran, ACT, Australia.
²¹ 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.
²² Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia; Monash Genetics, Monash Health, Clayton, Victoria, Australia.
²³ Genetics of Learning Disability Service, Hunter Genetics, Waratah, New South Wales, Australia.
²⁴ Department of Clinical Genetics, The Canberra Hospital, Garran, ACT, Australia.
²⁵ Genetics of Learning Disability Service, Hunter Genetics, Waratah, New South Wales, Australia; The University of Newcastle, Callaghan, New South Wales, Australia.
²⁶ Department of Clinical Genetics, Liverpool Hospital, Liverpool, New South Wales, Australia.
²⁷ Department of Clinical Genetics, Nepean Hospital, Kingswood, New South Wales, Australia.
²⁸ Department of Genomic Medicine, Westmead Hospital, Westmead, New South Wales, Australia.
²⁹ Sullivan Nicolaides Pathology, Bowen Hills, Queensland, Australia.
³⁰ Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia.
³¹ 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.
³² Forster Genetics, Forster, New South Wales, Australia.
³³ 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.
³⁴ Monash Genetics, Monash Health, Clayton, Victoria, Australia; Department of Paediatrics, Monash University, Clayton, Victoria, Australia.
³⁵ Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; The Royal Melbourne Hospital, Parkville, Victoria, Australia.
³⁶ 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.
³⁷ NSW Health Pathology, Randwick, New South Wales, Australia; Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia.
³⁸ 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.
³⁹ 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.
⁴⁰ 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.
⁴¹ Department of Pathology, University of Melbourne, Parkville, Victoria, Australia; Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, Victoria, Australia.
⁴² 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.
⁴³ 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.
⁴⁴ 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.
⁴⁵ Rare Diseases Functional Genomics, Kids Research, Sydney Children's Hospital Network and Children's Medical Research Institute, Westmead, New South Wales, Australia.
⁴⁶ School of Medicine, The University of Auckland, Auckland, New Zealand.
⁴⁷ Department of Neurology, Auckland City Hospital, Auckland, New Zealand.
⁴⁸ Center for Clinical Genetics, Sydney Children's Hospital, Randwick, New South Wales, Australia.
⁴⁹ 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.
⁵⁰ Department of Clinical Genetics, The Children's Hospital at Westmead, Westmead, New South Wales, Australia.
⁵¹ 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.
⁵² 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.
⁵³ 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.
⁵⁴ 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.
⁵⁵ Molecular Otolaryngology and Renal Research Laboratories, Carver College of Medicine, University of Iowa, Iowa City, IA, United States.
⁵⁶ Department of Paediatrics, Monash University, Clayton, Victoria, Australia.
⁵⁷ Fulgent Genetics, Temple City, CA.
⁵⁸ Department of Neurogenetics, Kolling Institute, Faculty of Medicine and Health, University of Sydney, Royal North Shore Hospital, St Leonards, New South Wales, Australia.
⁵⁹ Department of Paediatrics, Monash University, Clayton, Victoria, Australia; Monash Newborn, Monash Children's Hospital, Clayton, Victoria, Australia.
⁶⁰ 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.
⁶¹ Department of Pathology, The Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia.
⁶² Department of Medicine, University of Melbourne, Parkville, Victoria, Australia; Department of Genomic Medicine, The Royal Melbourne Hospital, Parkville, Victoria, Australia.
⁶³ Department of Clinical Genetics, Royal North Shore Hospital, St Leonards, New South Wales, Australia.
⁶⁴ Mater Research Institute, The University of Queensland, South Brisbane, Queensland, Australia.
⁶⁵ 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.
⁶⁶ 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.
⁶⁷ Northern Hub, Genetic Health Service NZ, Auckland, New Zealand.
⁶⁸ Department of Intensive Care, Austin Hospital, Heidelberg, Victoria, Australia.
⁶⁹ 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.

PMID: 34906502
DOI: 10.1016/j.gim.2021.09.001

Abstract

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.

Keywords: Genetic diagnosis; Noncoding variant; Pre-mRNA splicing; Putative splice variant; Variant classification.

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Conflict of interest statement

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.

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

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

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