Gregory Costain

Background: Allele-specific antisense oligonucleotides (ASOs) are increasingly used to selectively suppress transcripts containing pathogenic gain-of-function or dominant negative (GOF/DN) variants. However, most current approaches rely on patient-specific target selection of SNVs in cis with the disease-causing variant. This individualized approach may limit broader ASO applicability and could exacerbate inequities in access. Population-level selection of ASO-targetable SNVs is an alternative approach not previously explored at scale. Methods: For a curated set of >400 disease genes with putative toxic GOF/DN mechanisms, we applied a greedy algorithm to identify ASO-targetable SNVs that maximize population coverage in the 1000 Genomes Project dataset. Population coverage was evaluated across ″superpopulation″ ancestry groups and assessed in multiple diverse replication datasets. For each prioritized SNV we attempted to design allele-specific 15-mer and 20-mer ASOs meeting standard chemistry and sequence criteria. The presence of prioritized SNVs was assessed in two local cohorts with GOF/DN disorders: infants with epilepsy diagnosed by rapid short-read genome sequencing, and children with long-read genome sequencing data generated for bespoke ASO development. Results: We identified 7,927 SNVs (median 17.5 per gene) achieving a median cumulative heterozygous population coverage of 88.9% across 408 disease genes. More than two-thirds of genes (70.6%) reached ≥80% coverage using a median of only four prioritized SNVs. Coverage was consistently high for all ″superpopulation″ ancestry groups, with median coverage proportions of ≥85%. Prioritized SNVs generalized to independent ancestrally diverse replication datasets, achieving median coverage of 86.4% in the Human Genome Diversity Project and 90.3% in the All of Us Research Program . Many prioritized targets were compatible with established ASO design principles, enabling generation of candidate allele-specific 15-mer and 20-mer ASOs at scale for future experimental validation. The presence of prioritized targets in the rapid short-read sequencing cohort, and the overlap between prioritized targets and manually curated long-read genome sequencing targets, supports the clinical relevance of population-informed target selection. All SNV targets and candidate allele-specific ASO sequences are available at hawk-eye.research.sickkids.ca/knockdown. Conclusions: Prioritization of common SNV targets may facilitate the development of ASO therapies with broader population coverage, helping move the field beyond single-patient applications and toward more equitable opportunities for access.

Purpose: To describe the development of - and outcomes from - an institution-level initiative supporting access to innovative genetic medicines information and opportunities. Methods: We developed and implemented a Genetic Medicines Patient Assessment Pathway for rare genetic conditions at a large public hospital, with multidisciplinary teams collaborating to evaluate a patient’s molecular and clinical amenability to experimental and/or to-be-developed genetic medicines (primarily nucleic acid therapeutics). A Genetic Medicines Consult Clinic operating in parallel offered no-cost specialized consultations and counseling to families regarding genetic medicines inquiries and Pathway outcomes. We retrospectively reviewed submissions, decisions, and outcomes over a >2-year period. Results: A total of 63 submissions were reviewed in the Patient Assessment Pathway. Most submissions were classified as eligible or potentially eligible for at least one genetic medicines approach (42/63; 67%). Recommendations generated 87 discrete actions, such as outreach to potential collaborators (n = 28), offering participation in existing research studies (n = 23), or referral to the Consult Clinic (n = 19). Two patients have been approved for therapeutic program initiation or clinical trial enrolment. Conclusion: Findings to date support feasibility and high uptake of a structured, multidisciplinary, medical genetics-led model for assessing patient-level opportunities for genetic medicines.

Antisense oligonucleotides (ASOs) are a versatile therapeutic modality for inborn genetic diseases. ASOs can induce skipping of “dispensable” exons containing disease-causing variants to rescue protein amount and function, but this approach has been studied for only a small number of genes. We developed a high-throughput in silico tool for assessing exon dispensability and designing exon-skipping ASO sequences. Parameters were optimized using known dispensable and in-frame indispensable exons. Across 72,644 exons of 5,057 disease genes, we identified thousands of new targets for exon-skipping ASOs (3.4% of exons with most stringent filters, 24.5% with less stringent filters) that collectively include 0.97%-15.6% of disease-causing variants in large-scale databases. To facilitate recognition of DNA variants potentially amenable to exon skipping as a therapeutic strategy, we established the HAWK-EYE database as a repository of exon dispensability predictions and corresponding in silico -optimized ASO sequences, available as an open-access web application ( https://hawk-eye.research.sickkids.ca/ ). To illustrate translational utility, we experimentally validated a subset of the in silico -optimized ASO sequences that were generated for all Dispensable exons in the HAWK-EYE database, and showed that skipping a Dispensable exon in SOX5 preserves protein function using in vivo and in vitro assays. This scalable platform approach to exon-skipping ASOs will accelerate identification and testing of amenable genetic variants.

The PM5 rule in the 2015 ACMG/AMP variant classification guidelines applies to missense variants at an amino acid position where a different missense varia

The highest incidence of epilepsy in childhood occurs in the first year of life. Infantile epilepsies are associated with substantial morbidity and mortality. Although most are presumed to have genetic etiologies, many infants with nonacquired epilepsy remain genetically unsolved after clinical genome sequencing. The yield of reanalysis after nondiagnostic genome sequencing in this population is unknown. We aimed to determine the diagnostic yield of comprehensive reanalysis after nondiagnostic genome sequencing in infants with unexplained epilepsy. This cohort study included infants with unexplained epilepsy or complex febrile seizures who were recruited from 4 pediatric referral centers from September 2021 to March 2024 and had nondiagnostic clinical rapid genome sequencing. We performed comprehensive reanalysis of genome sequencing data from infants and available biological parents using multiple bioinformatics pipelines through July 2025 and clinically confirmed reanalysis findings. The primary outcome was diagnostic yield of genome sequencing reanalysis, defined as the percentage of infants who received genetic diagnoses from reanalysis. The secondary outcome was clinical utility of reanalysis findings. From an initial cohort of 312 infants with unexplained epilepsy who underwent clinical rapid genome sequencing, we performed comprehensive genome reanalysis in 176 infants with initially nondiagnostic results at a median age of 642 days, including 63 female patients (36%) and 30 (17%) with neonatal-onset seizures. The diagnostic yield of reanalysis was 5.1% (9/176, 95% CI 2.4%-9.5%), increasing the overall yield from 43.6% (136/312, 95% CI 38.0%-49.3%) to 46.5% (145/312, 95% CI 40.8%-52.2%). Of the new diagnoses, 6 involved variants not reported by clinical laboratories (2 single nucleotide variants, 2 structural variants, 1 tandem repeat expansion, 1 mosaic variant) and 3 involved previously reported variants of uncertain significance with new evidence. All diagnoses had clinical utility. Comprehensive reanalysis after nondiagnostic rapid genome sequencing has utility for infants with unexplained epilepsy. Our findings support implementation of reanalysis within 1-2 years after nondiagnostic genomic sequencing into routine clinical care of children with unexplained epilepsy and the expansion of clinically accredited genomic sequencing to include complex and noncoding variant detection.

Spliceosomopathies are syndromes caused by pathogenic variants in genes involved in splicing and mRNA metabolism. Here, we report a novel spliceosomopathy

Mendel's law of equal segregation states that during gamete formation, the 2 alleles at a gene locus segregate such that each gamete has an equal probability of containing either allele. Transmission ratio distortion (TRD) occurs when 1 of the 2 alleles from either parent is preferentially transmitted to the offspring, resulting in a deviation from the expected 1:1 ratio. Although TRD has been observed and studied in nonhuman species, the full extent and underlying biology of TRD in humans remains poorly summarized. Here we present a systematic review to assess evidence of TRD in the human genome, tracing reports from the 1970s through 2025. Overall, 96 studies including 42 different human variants/genes/loci met inclusion criteria. These studies provided only preliminary and/or conflicting evidence of TRD. Study methods were limited by multiple recurrent biases. Experimental validation of the biological mechanism(s) underlying the putative distortion was rarely performed or possible. TRD warrants renewed attention in the field of human genetics, especially with the growing availability of very large, family-based genome-wide sequencing datasets.

Neurodevelopmental proteasomopathies are a group of disorders caused by variants in proteasome subunit genes, that disrupt protein homeostasis and brain development through poorly characterized mechanisms. Here, we report 26 distinct variants in PSMC5 , encoding the AAA⁺ ATPase subunit PSMC5/RPT6, in individuals with syndromic neurodevelopmental conditions. Combining genetic, multi-omics and biochemical approaches across cellular models and Drosophila , we unveil the essential role of proteasomes in sustaining key cellular processes. Loss of PSMC5/RPT6 function impairs proteasome activity, leading to protein aggregation, disruption of mitochondrial homeostasis, and dysregulation of lipid metabolism and immune signaling. It also compromises synaptic balance, neuritogenesis, and neural progenitor cell stemness, causing deficits in higher-order functions, including learning and locomotion. Pharmacological targeting of integrated stress response kinases reveals a mechanistic link between proteotoxic stress and spontaneous type I interferon activation. These findings expand our understanding of proteasome-dependent quality control in neurodevelopment and suggest potential therapeutic strategies for neurodevelopmental proteasomopathies.

Objectives: Genome-wide sequencing (GWS) is now used across the breadth of pediatric research. There is a greater potential to identify unexpected, clinically relevant findings with GWS than with the targeted genetic techniques used in prior decades. Individual research teams may not have the expertise to evaluate and manage these findings. The Hospital for Sick Children (SickKids) Genome Board is a no-cost consultation service for researchers with questions arising from genetic aspects of their studies. Methods: We reviewed all submissions to and recommendations from the Genome Board over the first 4 years, to identify common questions, themes, and trends. Results: There were 67 submissions and a year-over-year increase in volumes. The most common request (60%) was to assess variants identified by GWS for pathogenicity, clinical actionability, and returnability to a study participant. Overall, 23 of 48 reviewed variants were recommended for clinical confirmation and return with genetic counselling. Other categories of submissions included requests to researchers from study participants to release their “raw” genomic data and for input on protocols related to clinical translation of findings. Conclusion: The Genome Board provides a generalizable model for centralized triage of clinical questions arising from genomic research at a pediatric centre. Clinicians should be aware that patient participation in genetic research studies can have downstream consequences for their healthcare.