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1. A multitiered analysis platform for genome sequencing: Design and initial findings of the Australian Genomics Cardiovascular Disorders Flagship

Author

Rachel Austin, Jaye S. Brown, Sarah Casauria, Evanthia O. Madelli, Tessa Mattiske, Tiffany Boughtwood, Alejandro Metke, Andrew Davis, Ari E. Horton, David Winlaw, Debjani Das, Magdalena Soka, Eleni Giannoulatou, Emma M. Rath, Eric Haan, Gillian M. Blue, Jitendra Vohra, John J. Atherton, Karin van Spaendonck-Zwarts, Kathy Cox, Leslie Burnett, Mathew Wallis, Matilda Haas, Michael C.J. Quinn, Nicholas Pachter, Nicola K. Poplawski, Zornitza Stark, Richard D. Bagnall, Robert G. Weintraub, Sarah-Jane Pantaleo, Sebastian Lunke, Paul De Fazio, Tina Thompson, Paul James, Yuchen Chang, Diane Fatkin, Ivan Macciocca, Jodie Ingles, Sally L. Dunwoodie, Chris Semsarian, Julie McGaughran, Lesley Ades, Annabel Enriquez, Alison McLean, Renee Smyth, Dimithu Alankarage, James McNamara, Morgan almog, Vanessa Fear, Caroline Medi, Mohammad Al-Shinnag, Miriam Fine, Raymond Sy, Keri Finlay, Di Milnes, Dotti Tang, Denisse Garza, Michael Milward, Jessica Taylor, Ansley Morrish, Shelby Taylor, Chris Barnett, Laura Gongolidis, Jim Morwood, Michel Tchan, Belinda Gray, Helen Mountain, Simon Bodek, Cassie Greer, David Mowat, Jordan Thorpe, Kirsten Boggs, Chai-Ann Ng, Alison Trainer, Michael Bogwitz, Mathilda Haas, Natalie Nowak, Gunjan Trivedi, Bernadette Hanna, Noelia Nunez Martinez, Giulia Valente, Alessandra Bray, Richard Harvey, Monique Ohanian, Marie-Jo Brion, Janette Hayward, Sinead O’Sullivan, Jamie Vandenberg, Jaye Brown, Carmen Herrera, Angela Overkov, Kunal Verma, Rob Bryson Richardson, Adam Hill, Miranda Vidgen, Georgie Hollingsworth, Chirag Patel, Charlotte Burns, Georgina Hollway, Mark Perrin, Kathryn Waddel-Smith, Michelle Cao, Matthew Perry, Will Carr, Denise Howting, Andreas Pflaumer, Peta Phillips, Meredith Wilson, Heather Chalinor, Joanne Isbister, Thuan Phuong, Matilda Jackson, Rachel Pope-Couston, Lisa Worgan, Gavin Chapman, Linda Wornham, Theosodia Charitou, Sarah Jane-Pantaleo, Preeti Punni, Kathy Wu, Belinda Chong, Renee Johnson, Laura Yeates, Felicity Collins, Andrew Kelly, Michael Quinn, Dominica Zentner, Gemma Correnti, Sarah King-Smith, Sulekha Rajagopalan, Edwin Kirk, Hariharan Raju, Fiona Cunningham, Sarah Kummerfeld, Timo Lassman, Matthew Regan, Jason Davis, Jonathon Lipton, Jonathan Rogers, Mark Ryan, Sarah Sandaradura, Michelle de Silva, Paul MacIntyre, Nicole Schonrock, Nicola Den Elzen, Paul Scuffham, Sophie Devery, Amali Mallawaarachchi, Julia Dobbins, Julia Mansour, Isabella Sherburn, Ellenore Martin, Mary-Clare Sherlock, Nathan Dwyer, Jacob Mathew, Emma Singer, Stefanie Elbracht-Leong, Carla Smerdon, David Elliott, and Janine Smith

Subjects
Australian Genomics, Cardiovascular genetic disorders, Genome sequencing, Specialized multidisciplinary care, Genetics, QH426-470, Medicine
Abstract

Purpose: The Australian Genomics Cardiovascular Disorders Flagship was a national multidisciplinary collaboration. It aimed to investigate the feasibility of genome sequencing (GS) and functional genomics to resolve variants of uncertain significance (VUS) in the clinical management of patients and families with cardiomyopathies, primary arrhythmias, and congenital heart disease (CHD). Methods: Between April 2019 and December 2021, 600 probands meeting cardiovascular disorder criteria from 17 cardiology and genetics clinics across Australia were enrolled in the Flagship and underwent GS. The Flagship adopted a tiered approach to GS analysis. Tier 1 analysis assessed genes with established clinical validity for each cardiovascular condition. Tier 2 analysis assessed lesser-evidenced research-based genes. Tier 3 analysis assessed the functional impact of VUS that remained after tier 1 and tier 2 analysis. Results: Overall, a pathogenic or likely pathogenic variant was identified in 41% of participants with a cardiomyopathy, 40% with an arrhythmia syndrome, and 15% with a familial CHD/CHD+Extra Cardiac Anomalies. A VUS outcome ranged from 13% for arrhythmias to 34% for CHD/CHD+Extra Cardiac Anomalies participants. Tier 2 research analysis identified a likely pathogenic/pathogenic variant for a further 15 participants and a VUS for an additional 15 participants. Conclusion: The Flagship successfully facilitated a model of care that harnesses clinical GS and functional genomics for the resolution of VUS in the clinical setting. This valuable data set can be used to inform clinical practice and facilitate research into the future.

Published
2024
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2. Birt-Hogg-Dubé Syndrome and Hereditary Leiomyomatosis and Renal Cell Carcinoma Syndrome: An Effective Multidisciplinary Approach to Hereditary Renal Cancer Predisposing Syndromes

Author

Mohammad Al-Shinnag, Helen Marfan, Rachel Susman, Jan Wakeling, Sonja Gustafson, Simon Wood, and Andrew John Mallett

Subjects
renal cell cancer, Birt-Hogg-Dubé syndrome, hereditary leiomyoma and renal cell carcinoma syndrome, surveillance, multidisciplinary (care or team), Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

AimWe aimed to describe and analyse clinical features, characteristics, and adherence to surveillance guidelines in an Australian Birt-Hogg-Dubé syndrome (BHD) and hereditary leiomyomatosis and renal cell cancer (HLRCC) cohort.MethodsAll identified patients with a diagnosis of BHD or HLRCC at RBWH 01/01/2014-01/09/2019 were included (HREC/17/QRBW/276). All patients were initially assessed and counselled by a clinical geneticist and then referred to an adult nephrologist. Baseline and incidental clinical variables were extracted and analysed.ResultsFifty-seven patients were identified (28 BHD, 29 HLRCC) with a median age of 47 years. The median and cumulative follow-up were 1 and 99 years, respectively. Baseline renal MRI occurred in 40/57 patients, and 33/57 had regular MRI as per the national guidelines (eviQ). Of 18/57 without baseline imaging, nine were yet to have imaging, seven were lost follow-up, and two patients had logistic difficulties. RCC was diagnosed in 11/57 patients: two of 28 with BHD were diagnosed with RCC aged 73 and 77, both prior to commencement of surveillance. Nine of 29 patients with HLRCC were diagnosed with RCC (one of 29 during surveillance at 47 years of age) and eight of 29 prior to commencement of surveillance (11–55 years). Amongst BHD patients, cutaneous fibrofolliculomas were noted in 15 patients, lung cysts were detected in seven patients, spontaneous pneumothoraces in five patients, and parotid oncocytoma in two of 28. Amongst those with HLRCC, cutaneous leiomyomas were noted in 19/29, cutaneous leiomyosarcoma diagnosed in one of 29, and uterine fibroids in 13 female patients.ConclusionEvidence-based RCC screening in BHD and HLRCC cohort is feasible and able to identify incidental renal lesions. Multidisciplinary patient management enables expedited genetic counselling, diagnosis, longitudinal screening, and RCC management. The success of this clinical model warrants consideration of undertaking longitudinal screening of BHD and HLRCC patients by nephrologists.

Published
2021
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3. A translation re-initiation variant in KLHL24 also causes epidermolysis bullosa simplex and dilated cardiomyopathy via intermediate filament degradation

Author

Mathilde C.S.C. Vermeer, Mohammad Al-Shinnag, Herman H.W. Silljé, Antonio Esquivel Gaytan, Dedee F. Murrell, Julie McGaughran, Wei Melbourne, Timothy Cowan, Peter C. van den Akker, Karin Y. van Spaendonck-Zwarts, Peter van der Meer, Maria C. Bolling, Human Genetics, ACS - Heart failure & arrhythmias, Cardiovascular Centre (CVC), Translational Immunology Groningen (TRIGR), and Restoring Organ Function by Means of Regenerative Medicine (REGENERATE)

Subjects
Cardiomyopathy, Dilated, Phenotype, Epidermolysis Bullosa Simplex, Mutation, Intermediate Filaments, Humans, Codon, Initiator, Dermatology
Abstract

This study shows that gain-of-function variants in KLHL24 causing EBS and DCM, do not only originate in the start-codon and suggest that any nonsense-inducing variant affecting nucleotides c.4_84 will likely cause the same effect on protein level and a similar potential lethal phenotype.

Published
2022

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

Author

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

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