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7 results on '"Shobhana Bommireddipalli"'

1. Severe NAD(P)HX Dehydratase (NAXD) Neurometabolic Syndrome May Present in Adulthood after Mild Head Trauma

Author

Nicole J. Van Bergen, Karen Gunanayagam, Adam M. Bournazos, Adhish S. Walvekar, Marc O. Warmoes, Liana N. Semcesen, Sebastian Lunke, Shobhana Bommireddipalli, Tim Sikora, Myrto Patraskaki, Dean L. Jones, Denisse Garza, Dale Sebire, Samuel Gooley, Catriona A. McLean, Parm Naidoo, Mugil Rajasekaran, David A. Stroud, Carole L. Linster, Mathew Wallis, Sandra T. Cooper, and John Christodoulou

Subjects
NAXD deficiency, NAXE deficiency, metabolite repair, metabolism, febrile illness, oral ulcers, Biology (General), QH301-705.5, Chemistry, QD1-999
Abstract

We have previously reported that pathogenic variants in a key metabolite repair enzyme NAXD cause a lethal neurodegenerative condition triggered by episodes of fever in young children. However, the clinical and genetic spectrum of NAXD deficiency is broadening as our understanding of the disease expands and as more cases are identified. Here, we report the oldest known individual succumbing to NAXD-related neurometabolic crisis, at 32 years of age. The clinical deterioration and demise of this individual were likely triggered by mild head trauma. This patient had a novel homozygous NAXD variant [NM_001242882.1:c.441+3A>G:p.?] that induces the mis-splicing of the majority of NAXD transcripts, leaving only trace levels of canonically spliced NAXD mRNA, and protein levels below the detection threshold by proteomic analysis. Accumulation of damaged NADH, the substrate of NAXD, could be detected in the fibroblasts of the patient. In agreement with prior anecdotal reports in paediatric patients, niacin-based treatment also partly alleviated some clinical symptoms in this adult patient. The present study extends our understanding of NAXD deficiency by uncovering shared mitochondrial proteomic signatures between the adult and our previously reported paediatric NAXD cases, with reduced levels of respiratory complexes I and IV as well as the mitoribosome, and the upregulation of mitochondrial apoptotic pathways. Importantly, we highlight that head trauma in adults, in addition to paediatric fever or illness, may precipitate neurometabolic crises associated with pathogenic NAXD variants.

Published
2023
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3. SpliceVault predicts the precise nature of variant-associated mis-splicing

Author

Ruebena Dawes, Adam M. Bournazos, Samantha J. Bryen, Shobhana Bommireddipalli, Rhett G. Marchant, Himanshu Joshi, and Sandra T. Cooper

Subjects
Genetics
Abstract

Even for essential splice-site variants that are almost guaranteed to alter mRNA splicing, no current method can reliably predict whether exon-skipping, cryptic activation or multiple events will result, greatly complicating clinical interpretation of pathogenicity. Strikingly, ranking the four most common unannotated splicing events across 335,663 reference RNA-sequencing (RNA-seq) samples (300K-RNA Top-4) predicts the nature of variant-associated mis-splicing with 92% sensitivity. The 300K-RNA Top-4 events correctly identify 96% of exon-skipping events and 86% of cryptic splice sites for 140 clinical cases subject to RNA testing, showing higher sensitivity and positive predictive value than SpliceAI. Notably, RNA re-analyses showed we had missed 300K-RNA Top-4 events for several clinical cases tested before the development of this empirical predictive method. Simply, mis-splicing events that happen around a splice site in RNA-seq data are those most likely to be activated by a splice-site variant. The SpliceVault web portal allows users easy access to 300K-RNA for informed splice-site variant interpretation and classification.

Published
2023

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

5. Clinical impact of whole-genome sequencing in patients with early-onset dementia

Author

Aamira J Huq, Bryony Thompson, Mark F Bennett, Adam Bournazos, Shobhana Bommireddipalli, Alexandra Gorelik, Joshua Schultz, Adrienne Sexton, Rebecca Purvis, Kirsty West, Megan Cotter, Giulia Valente, Andrew Hughes, Moeen Riaz, Maie Walsh, Sarah Farrand, Samantha M Loi, Trevor Kilpatrick, Amy Brodtmann, David Darby, Dhamidhu Eratne, Mark Walterfang, Martin Bruce Delatycki, Elsdon Storey, Michael Fahey, Sandra Cooper, Paul Lacaze, Colin L Masters, Dennis Velakoulis, Melanie Bahlo, Paul A James, and Ingrid Winship

Subjects
Psychiatry and Mental health, Neurology & Neurosurgery, 11 Medical and Health Sciences, 17 Psychology and Cognitive Sciences, Surgery, Neurology (clinical)
Abstract

BackgroundIn the clinical setting, identification of the genetic cause in patients with early-onset dementia (EOD) is challenging due to multiple types of genetic tests required to arrive at a diagnosis. Whole-genome sequencing (WGS) has the potential to serve as a single diagnostic platform, due to its superior ability to detect common, rare and structural genetic variation.MethodsWGS analysis was performed in 50 patients with EOD. Point mutations, small insertions/deletions, as well as structural variants (SVs) and short tandem repeats (STRs), were analysed. An Alzheimer’s disease (AD)-related polygenic risk score (PRS) was calculated in patients with AD.ResultsClinical genetic diagnosis was achieved in 7 of 50 (14%) of the patients, with a further 8 patients (16%) found to have established risk factors which may have contributed to their EOD. Two pathogenic variants were identified through SV analysis. No expanded STRs were found in this study cohort, but a blinded analysis with a positive control identified aC9orf72expansion accurately. Approximately 37% (7 of 19) of patients with AD had a PRS equivalent to >90th percentile risk.DiscussionWGS acts as a single genetic test to identify different types of clinically relevant genetic variations in patients with EOD. WGS, if used as a first-line clinical diagnostic test, has the potential to increase the diagnostic yield and reduce time to diagnosis for EOD.

Published
2021

6. Digenic Inheritance Involving a Muscle Specific Protein Kinase and the Giant Titin Protein Causes a Skeletal Muscle Myopathy

Author

Ana Topf, Irina Zaharieva, Valeria Di Leo, Anna Vihola, Neha Wali, Marco Savarese, Kristen Laricchia, Cristina Venturini, Bas Vroling, Beryl Cummings, Rita Barresi, Elizabeth Harris, Chiara Marini Bettolo, Dan Cox, Jennifer Duff, Eleina England, Jane Patrick, Valerie Biancalana, Shobhana Bommireddipalli, Carsten Bonnemann, Anita Cairns, Mei Chiew, Kristl G. Claeys, Sandra Cooper, Mark R. Davis, Sandra Donkervoort, Corrie E. Erasmus, Carla Grosmann, Heinz Jungbluth, Erik-Jan Kamsteeg, Xaviere Lornage, Wolfgang Löscher, Edoardo Malfatti, Adnan Manzur, Pilar Marti, Tiziana Mongini, Nuria Muelas, Atsuko Nishikawa, Narumi Ogonuki, Gina O'Grady, Stephanie Paquay, Rahul Phadke, Beth Pletcher, Norma Romero, Meyke Schouten, Snehal Shah, Yves Sznajer, Giorgio Tasca, Allysa Tuite, Peter van den Bergh, Nicol Voermans, Julia Wanschitz, Elizabeth Wraige, Kimihiko Yoshimura, Emily Oates, Osamu Nakagawa, Ichizo Nishino, Jocelyn Laporte, Juan Vilchez, Daniel Macarthur, Anna Sarkozy, Bjarne Udd, Elisabeth Busch-Nentwich, Francesco Muntoni, and Volker Straub

Published
2021

7. Two novel B9D1 variants causing Joubert syndrome: Utility of mRNA and splicing studies

Author

Disha Katiyar, Neil Anderson, Sandra T. Cooper, Himanshu Goel, Shobhana Bommireddipalli, and Adam Bournazos

Subjects
RNA Splicing, Mutation, Missense, Retina, Joubert syndrome, Young Adult, Cerebellum, Genetics, medicine, Humans, Abnormalities, Multiple, Eye Abnormalities, Genetic Testing, RNA, Messenger, Sonic hedgehog, Meckel syndrome, Genetics (clinical), biology, Cilium, Wnt signaling pathway, General Medicine, Kidney Diseases, Cystic, medicine.disease, Hypotonia, Cytoskeletal Proteins, Ciliopathy, RNA splicing, biology.protein, Female, medicine.symptom
Abstract

The primary cilium is an organelle which plays an important role in the transduction of signals in the Wnt and Sonic hedgehog pathways. Abnormal or absent primary cilia result in various neurodevelopmental, retinal, renal, hepatic and musculoskeletal abnormalities. Joubert syndrome (JS) is a ciliopathy with a prevalence estimated to be between 1:80 000 and 1:100 000. JS occurs due to bi-allelic mutations in one of the 34 identified genes, all of which encode for protein components of the primary cilia. The presentation of JS is highly variable, however a clinical diagnosis can be established by the presence of the molar tooth sign on axial brain MRI, hypotonia in infancy, and developmental delay. JS is less severe than Meckel syndrome (MKS), which is another recessive, and often lethal, ciliopathy. This report outlines an interesting case of JS, in which two novel mutations in B9D1 were identified. This gene is not commonly associated with JS, and is often implicated in MKS. Functional mRNA study was helpful in delineating the pathogenic role of novel variants in this case.

Published
2020

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