Authors :
Presenting Author: Emma Sherrill, BA – Boston Children's Hospital
David Cheerie, MSc – SickKids
Cara Beck, MD, PhD – Murdoch Children's Research Institute
Ella Whittle, PhD – UCL Great Ormond Street Institute of Child Health
Yasin Shafi, MSc – UCL Great Ormond Street Institute of Child Health
Gene-STEPS Study Group, N/A – International Precision Child Health Partnership
J. Helen Cross, M.B., Ch.B., PhD – University College London NIHR BRC Great Ormond Street Institute of Child Health
Ingrid Scheffer, AO MBBS PhD FRACP FAES FAA FRS – Epilepsy Research Centre and Royal Children’s Hospital, The University of Melbourne, Austin Health, Florey and Murdoch Children’s Research Institutes
Vann Chau, MD – SickKids
Tim Yu, MD, PhD – Harvard Medical School
Haiyan Zhou, MD, PhD – UCL Great Ormond Street Institute of Child Health
John Christodoulou, MBBS, PhD – Murdoch Children's Research Institute
Annapurna Poduri, MD, MPH – Boston Children's Hospital
Sarah Stephenson, PhD – Murdoch Children's Research Institute, Australia
Katherine Howell, MBBS, PhD – The University of Melbourne, Royal Children’s Hospital, Neuroscience Research Group, Murdoch Children's Research Institute
Amy McTague, MBChB, PhD – UCL Great Ormond Street Hospital for Children
Gregory Costain, MD, PhD – SickKids
Alissa D'Gama, MD, PhD – Boston Children's Hospital
Rationale:
Most neonatal and infantile onset epilepsies have presumed genetic etiologies. However, treatment remains largely empiric and outcomes are poor due to limited precision diagnoses and a gap from precision diagnoses to precision therapies. Gene-STEPS is an international multi-center study of rapid genome sequencing (rGS) in infants with unexplained epilepsy, with a 43% diagnostic yield in our first year of enrollment (D’Gama et al., Lancet Neurol, 2023, 22: 812-825). Here, we aimed to screen identified pathogenic variants for amenability to precision antisense oligonucleotide (ASO) therapies.
Methods:
For enrolled infants who received genetic diagnoses from rGS, we assessed the identified variants for ASO amenability using guidelines from the N=1 Collaborative (Cheerie et al., Am J Hum Genet, 2025, 112: 975-983) and a splice-modulating framework developed at Boston Children’s Hospital (Kim et al., Nature, 2023, 619: 828-836). Eligibility was determined based on several factors, including variant inheritance, pathomechanism, coding transcript position, and impact on pre-mRNA splicing and protein function.
Results:
We screened 141 variants from 132 infants with genetic epilepsies, which included 107 heterozygous, 16 homozygous, 2 hemizygous, and 8 pairs of compound heterozygous variants. One infant had a dual diagnosis. Most variants were single nucleotide variants or small insertions-deletions (62 missense, 31 frameshift, 22 nonsense, 5 intronic, 2 in-frame indels), 17 were copy number variants (4 intragenic), and 2 were repeat expansions. Overall, 16.3% of variants (23/141) were in principle eligible or likely eligible for an exon-skipping, knockdown, or existing upregulation ASO. One variant was possibly eligible for a splice-modulating ASO. Of the 24 infants with these variants, 41.7% (10/24) presented with developmental and epileptic encephalopathies, 12.5% (3/24) with self-limited epilepsy syndromes, and 45.8% (11/24) with other syndromes. An additional 17% of variants were potentially eligible for a novel upregulation ASO based on in silico database review but require further target validation. Further analysis will investigate the feasibility of therapy development in individual cases; for example, such therapies may not be appropriate for infants with self-limited epilepsies.
Conclusions:
These results highlight the potential for early precision diagnoses to expand early precision therapy options for neonatal and infantile epilepsies during a critical intervention window.
Funding:
Funding: AAP, Australia MRFF, AERF, BCH CRDC, BCH TRP, CIHR, Emma IS and Margaret R. Anderson endowment, Epilepsy Canada, Feiga Bresver Academic Fund, GOSH Charity, MRC, Melbourne Children's, MCRI, NHMRC, NICHD, NIHR GOSH BRC, NINDS, One8 Foundation, OBI, Robinson Family Initiative, Rosetrees Trust, The RCH Foundation, Thrasher Fund, University of Toronto McLaughlin Centre, Wellcome Trust, SickKids Foundation