Improving Diagnostic Yield in Epilepsy by Re-analysis of Short Read Genome Sequencing Data
Abstract number :
1.113
Submission category :
12. Genetics / 12A. Human Studies
Year :
2024
Submission ID :
1355
Source :
www.aesnet.org
Presentation date :
12/7/2024 12:00:00 AM
Published date :
Authors :
Presenting Author: Amy McTague, MBChB PhD – UCL Great Ormond Street Institute of Child Health
Maria Lachgar Ruiz, PhD – Great Ormond Street Hospital
Ted Higginbotham, BS – The Hospital for Sick Children, Toronto
Jimmy Nguyen, BS – SickKids Research Institute, Toronto
Katrina Bell, PhD – MCRI, Melbourne, Australia
Natalie Chandler, PhD – Great Ormond Street Hospital
Lyn Chitty, PhD – Great Ormond Street Hospital
John Coleman, MD PhD – MCRI, Melbourne, Australia
Matthew Coleman, PhD – MCRI, Melbourne, Australia
J. Helen Cross, MBChB, PhD – UCL-Great Ormond Street Institute of Child Health; Great Ormond Street Hospital
Anna Griffiths, PhD – MCRI, Melbourne, Australia
Britt Hanson, PhD – Great Ormond Street Hospital
Patrick Lombard, PhD – Great Ormond Street Hospital
Cristina Magro, BS – Great Ormond Street Hospital
Christian R Marshall, PhD – The Hospital for Sick Children, Toronto
Sarah Nesbitt, PhD – Great Ormond Street Hospital
Ben Paternoster, BS – Great Ormond Street Hospital
Ashley Pritchard, PhD – Great Ormond Street Hospital
Graham Rose, PhD – Great Ormond Street Hospital
Ingrid Scheffer, MBBS, PhD, FRACP, FRS – University of Melbourne, Austin Hospital and Royal Children's Hospital, Florey and Murdoch Children’s Research Institutes
Wanqing Shao, MD PhD – Harvard Medical School, Boston
Jashanpreet Sidhu, BSc – The Hospital for Sick Children
Sarah Stephenson, PhD – MCRI, Melbourne, Australia
Brett Trost, PhD – The Hospital for Sick Children, Toronto
GENE STEPS Study Group, PhD – SickKids Research Institute, Toronto
Vann Chau, MD – The Hospital for Sick Children
Katherine Howell, MBBS, PhD – Department of Neurology, Royal Children's Hospital, Melbourne, Australia
Annapurna Poduri, MD, MPH – Boston Children's Hospital
Zornitska Stark, PhD – Murdoch Children's Research Institute, Melbourne, Australia.
Gregory Costain, MD PhD – The Hospital for Sick Children, Toronto
Alissa D'Gama, MD, PhD – Boston Children's Hospital
Rationale: Accurate and timely genetic diagnosis in infantile-onset epilepsies is vital as it can dictate epilepsy management, including personalized medicine, and determine prognosis. Gene-STEPS is a multi-centre study examining the diagnostic yield and clinical utility of rapid trio genome sequencing (GS) in epilepsy patients < 12 months old. Primary analysis strategies revealed a 43% diagnostic yield in the first 100 patients. However, diagnostic laboratories face several challenges, such as variants in non-coding regions, calling of mosaic variants and detection and filtering of structural and mitochondrial variants. Here, we describe initial results of advanced interpretation strategies in short-read GS leading to increased diagnostic yield.
Methods: For Gene-STEPS participants without genetic diagnoses after clinical GS (n >170), we applied the following strategies: 1) re-evaluation of variants of uncertain significance using an agnostic approach, 2) manual review of GS data for a second variant including non-coding regions in cases with a single pathogenic variant in an autosomal recessive gene, 3) reanalysis of all coding SNVs and indels, including in a consensus epilepsy gene list (n=1,045), 4) assessment of additional variant types, such as mosaic, structural, and mitochondrial variants, and 5) targeted RNA-sequencing.
Results: Likely diagnoses were established in a further 15 patients, including candidate variants in disease-associated and potential novel genes. Further diagnoses included a complex structural variant (2.3 Mb inversion disrupting KMT2A), a mosaic variant (PIK3R2 present in 8.5% of reads), and a deep intronic variant in DNM1 confirmed with RNA sequencing to cause aberrant splicing.
Conclusions: Reanalysis improved yield from short-read GS in patients with infantile onset epilepsy, with significant impacts for patient management and reproductive counselling. With continuing improvements in bioinformatics pipelines and epilepsy gene discovery, regular re-analysis will be productive in unsolved patients.
Funding: BCH Children's Rare Disease Cohorts Initiative and the One8 Foundation. National Institute of Child Health and Human Development (T32 HD 098061) and the American Academy of Pediatrics (Marshall Klaus Neonatal-Perinatal Research Award). One8 Foundation, Robinson Family Initiative for Transformational Research, Canadian Institutes of Health Research (PJT186240); Epilepsy Canada; Feiga Bresver Academic Foundation; Ontario Brain Institute, University of Toronto McLaughlin Centre. (CRC-2021-00284). The Royal Children's Hospital Foundation. Melbourne Children's Clinician Scientist Fellowship. National Health and Medical Research Council (NHMRC) Centre for Research Excellence Grant. NHMRC Synergy Grant and Senior Investigator Grant, Australia Medical Research Future Fund, Australian Epilepsy Research Fund. MRC (MR/T007087/1), Great Ormond Street Hospital (GOSH) Charity (VS0122), Rosetrees Trust, and Wellcome Trust TIN Scheme. GOSH National Institute for Health and Care Research (NIHR) Biomedical Research Centre (BRC). Action Medical Research, British Paediatric Neurology Association Research Training Fellowship.
Genetics