1. Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants
- Author
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Adam M. Bournazos, Lisa G. Riley, Shobhana Bommireddipalli, Lesley Ades, Lauren S. Akesson, Mohammad Al-Shinnag, Stephen I. Alexander, Alison D. Archibald, Shanti Balasubramaniam, Yemima Berman, Victoria Beshay, Kirsten Boggs, Jasmina Bojadzieva, Natasha J. Brown, Samantha J. Bryen, Michael F. Buckley, Belinda Chong, Mark R. Davis, Ruebena Dawes, Martin Delatycki, Liz Donaldson, Lilian Downie, Caitlin Edwards, Matthew Edwards, Amanda Engel, Lisa J. Ewans, Fathimath Faiz, Andrew Fennell, Michael Field, Mary-Louise Freckmann, Lyndon Gallacher, Russell Gear, Himanshu Goel, Shuxiang Goh, Linda Goodwin, Bernadette Hanna, James Harraway, Megan Higgins, Gladys Ho, Bruce K. Hopper, Ari E. Horton, Matthew F. Hunter, Aamira J. Huq, Sarah Josephi-Taylor, Himanshu Joshi, Edwin Kirk, Emma Krzesinski, Kishore R. Kumar, Frances Lemckert, Richard J. Leventer, Suzanna E. Lindsey-Temple, Sebastian Lunke, Alan Ma, Steven Macaskill, Amali Mallawaarachchi, Melanie Marty, Justine E. Marum, Hugh J. McCarthy, Manoj P. Menezes, Alison McLean, Di Milnes, Shekeeb Mohammad, David Mowat, Aram Niaz, Elizabeth E. Palmer, Chirag Patel, Shilpan G. Patel, Dean Phelan, Jason R. Pinner, Sulekha Rajagopalan, Matthew Regan, Jonathan Rodgers, Miriam Rodrigues, Richard H. Roxburgh, Rani Sachdev, Tony Roscioli, Ruvishani Samarasekera, Sarah A. Sandaradura, Elena Savva, Tim Schindler, Margit Shah, Ingrid B. Sinnerbrink, Janine M. Smith, Richard J. Smith, Amanda Springer, Zornitza Stark, Samuel P. Strom, Carolyn M. Sue, Kenneth Tan, Tiong Y. Tan, Esther Tantsis, Michel C. Tchan, Bryony A. Thompson, Alison H. Trainer, Karin van Spaendonck-Zwarts, Rebecca Walsh, Linda Warwick, Stephanie White, Susan M. White, Mark G. Williams, Meredith J. Wilson, Wui Kwan Wong, Dale C. Wright, Patrick Yap, Alison Yeung, Helen Young, Kristi J. Jones, Bruce Bennetts, Sandra T. Cooper, Ghusoon Abdulrasool, Ghamdan Al Eryani, Peer Arts, Richard Bagnall, Naomi L. Baker, Christopher Barnett, Sarah Beecroft, Marina Berbic, Michael Black, Jim Blackburn, Piers Blombery, Susan Branford, Jimmy Breen, Leslie Burnett, Daffodil Canson, Pak Cheong, Edward Chew, John Christodoulou, Seo-Kyung Chung, Mike Clark, Corrina Cliffe, Melissa Cole, Felicity Collins, Alison Compton, Antony Cooper, Mark Corbett, Mark Cowley, Tracy Dudding, Stefanie Eggers, Eduardo Eyras, Miriam Fanjul Fernandez, Andrew Fellowes, Ron Fleischer, Chiara Folland, Lucy Fox, Clara Gaff, Melanie Galea, Roula Ghaoui, Ilias Gornanitis, Thuong Ha, Rippei Hayashi, Ian Hayes, Alex Henderson, Luke Hesson, Erin Heyer, Michael Hildebrand, Michael Hipwell, Cass Hoskins, Matilda Jackson, Paul James, Justin Jong-Leong Wong, Karin Kassahn, Peter Kaub, Lucy Kevin, Smitha Kumble, Sarah Kummerfeld, Nigel Laing, Chiyan Lau, Eric Lee, Sarah Leighton, Ben Lundie, Chelsea Mayoh, Julie McGaughran, Mary McPhillips, Cliff Meldrum, Edwina Middleton, Kym Mina, Amy Nisselle, Emily Oates, Alicia Oshlack, Gayathri Parasivam, Michael Parsons, Michael Quinn, John Rasko, Gina Ravenscroft, Anja Ravine, Krista Recsei, Jacqueline Rehn, Stephen Robertson, Anne Ronan, Georgina Ryland, Simon Sadedin, Andreas Schreiber, Hamish Scott, Rodney Scott, Christopher Semsarian, Cas Simons, Emma Singer, Renee Smyth, Amanda Spurdle, Patricia Sullivan, Samantha Sundercombe, David Thorburn, John Toubia, Ronald Trent, Emma Tudini, Irina Voneague, Leigh Waddell, Logan Walker, Mathew Wallis, Nick Warnock, Robert Weatheritt, Deborah White, Ingrid Winship, Lisa Worgan, Kathy Wu, Andrew Ziolowski, Bournazos, Adam M, Riley, Lisa G, Bommireddipalli, Shobhana, Ades, Lesley, Cooper, Sandra T, Toubia, John, and Australasian Consortium for RNA Diagnostics
- Subjects
Adult ,Adolescent ,RNA Splicing ,Genetic counseling ,putative splice variant ,Biology ,law.invention ,genetic diagnosis ,law ,Exome Sequencing ,Biopsy ,medicine ,Humans ,variant classification ,Gene ,Genetics (clinical) ,Polymerase chain reaction ,Genetics ,medicine.diagnostic_test ,Sequence Analysis, RNA ,noncoding variant ,RNA ,Heterozygote advantage ,Amplicon ,Child, Preschool ,Mutation ,RNA splicing ,pre-mRNA splicing - Abstract
usc Refereed/Peer-reviewed 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.
- Published
- 2022