Interventional genetics (IG) refers to the development of therapies aimed at treating the underlying genetic cause of disease. Diagnostic sequencing has advanced to the point where genetic results can be returned within weeks, meaning that therapeutically actionable variants associated with specific diseases could be developed immediately after diagnosis. Here, we describe 81 probands with a neurodevelopmental disorder (NDD) and family matched controls with full genotype/phenotype information and biobanked stem cells, most of which are consented for sharing. We outline a rapid and scalable pipeline for induced pluripotent stem cell (iPSC) generation directly from clinical collection, without the need for peripheral blood mononuclear cell (PBMC) storage, paired with induction to neurons. We provide a proof of principle for rapid creation of oligonucleotide therapeutics for Kleefstra syndrome. This work introduces a cohort of individuals with NDDs and an implemental pipeline to integrate IG with clinical diagnostics for NDDs. This information documents our experience and provides useful details for clinical centers interested in integrating IG for NDDs with diagnostic sequencing.

Recent expansion of large-scale biobank resources has enabled rare-variant association studies (RVASs) and systematic investigation of rare-variant pleiotropy across thousands of phenotypes simultaneously. However, existing statistical frameworks for dissecting pleiotropy were largely developed for common-variant association signals and are not well suited to gene-based rare-variant burden signals, limiting the interpretation of cross-phenotype associations. Here, we develop Allelic Spectrum of Pleiotropy Informed Correlated Effects (ALLSPICE), a likelihood-based method that tests whether rare coding variant effects in genes exhibiting cross-phenotype associations are proportional or heterogeneous across continuous traits while accounting for phenotypic correlation using summary statistics. ALLSPICE is well calibrated in simulations and is implemented as an R package for scalable analysis of gene-level rare-variant burden associations. We applied ALLSPICE to RVAS of 359 continuous traits in the UK Biobank and identified 124 significant heterogeneous events among 11,810 pairs of gene-trait associations. By identifying effect heterogeneity within genes associated with multiple phenotypes, ALLSPICE extends analysis of allelic heterogeneity to biobank-scale RVASs, clarifies shared and heterogeneous rare-variant architectures underlying cross-phenotype burden associations, and provides insight into rare-variant pleiotropy.

Brain-specific serine/threonine kinase (BRSK1; synapses of amphids defective [SAD]-B) encodes an AMP-activated protein kinase (AMPK)-related serine/threonine kinase required for neuronal polarization and synaptic function. An individual with a variant in BRSK1 was identified in the Texome Project, which provides genomic diagnosis to financially disadvantaged individuals in Texas, using AI-MARRVEL. We subsequently found nine individuals harboring rare heterozygous BRSK1 variants through GeneMatcher. Affected individuals present with developmental delay and variable phenotypes including anxiety, attention-deficit hyperactivity disorder (ADHD), autism, and seizures. All variants (missense and nonsense) are predicted to be deleterious by pathogenicity prediction tools. We utilized Drosophila to model three missense variants to assess the impact of the variants in vivo. We show that Drosophila sff (sugar-free frosting; ortholog of BRSK1) is expressed in neurons of the larval central nervous system (CNS) and adult brain. Loss of sff leads to viable flies with severe locomotor impairment, bang and heat sensitivity, and a short lifespan. In addition, the third-instar neuromuscular junctions (NMJs) in sff null mutants display a significant overgrowth, associated with elevated levels of Futsch (MAP1B), a microtubule-associated protein. Expression of the human reference BRSK1 cDNA in the sff null mutant rescues the behavioral, NMJ morphology, and Futsch phenotypes, showing that the human gene is functional in flies. In contrast, the three individual-derived alleles (BRSK1[p.Ile202Val], BRSK1[p.Arg237Cys], and BRSK1[p.Thr406Ile]) provide only a partial rescue and fail to normalize NMJ morphology and Futsch levels, suggesting that they are partial loss-of-function alleles. In summary, our data support a model that heterozygous loss of BRSK1 leads to a neurodevelopmental syndrome with variable phenotypes.

Next-generation sequencing has transformed diagnosis, prognosis, and treatment across rare disease, cancer, immunology, and infectious disease. As variant interpretation may evolve with emerging evidence, sharing genetic data is essential to improve diagnostic accuracy and advance genomic medicine. However, practical guidance for implementing clinical genetic data sharing remains limited. The Canadian College of Medical Geneticists (CCMG), therefore, developed national guidance to support secure, ethical, and effective genetic data sharing by Canadian clinical laboratories. An ad hoc CCMG working group with broad geographic and disciplinary representation developed the initial framework of this guidance through six meetings. Members included clinical laboratory geneticists, genomics specialists, a legal expert, a clinical geneticist, and a genetic counselor. The process drew on expert consensus (including patient and family perspectives), existing frameworks, and relevant peer-reviewed evidence, followed by iterative external review. Reporting was informed by the Appraisal of Guidelines for Research and Evaluation II (AGREE II) framework. The guidance provides recommendations to support genetic data sharing by Canadian clinical laboratories. It addresses benefits, risks, and ethical considerations, with emphasis on proportionality, privacy, and governance. Recommendations include approaches to sharing diverse genetic data types, establishing institutional policies, and addressing implementation barriers. This guidance aims to align Canadian clinical laboratory data-sharing practices with international standards and improve diagnostic accuracy, equity, and innovation in genomic medicine. By emphasizing ethical principles, proportionality, and governance, it seeks to enable responsible data sharing; strengthen trust among patients, families, and professionals; and contribute to the broader global genomic data ecosystem.

Detecting and interpreting epistatic effects in the human genome is essential for a complete understanding of the genetic architecture of gene regulation and complex traits. Progress in this area, however, has been hindered by limited discovery power and an abundance of false positives. Here, leveraging large-scale plasma proteomic data from the UK Biobank (UKB) Pharma Proteomics Project (PPP), we systematically map high-confidence cis-by-trans epistatic effects regulating protein expression. To reduce the multiple-testing burden, we focus on protein-level rather than variant-level interaction effects, and we employ a sandwich variance estimator to control false positives, as validated by extensive simulations. We applied the approach to identify cis-by-trans interactions across all proteins assayed in UKB-PPP and detected seven significant epistatic effects. Incorporating these interactions into protein-wide association studies is highly prone to false positives. We thus developed a principled framework but found that they offered little improvement in trait mapping power, likely because their effects on protein-expression variance are outweighed by additive effects. Analysis of the biological and evolutionary context of our detected epistatic interactions pointed to ABO as a central regulator that appears to modulate mean protein expression for several trans-chromosomal targets through its effects on blood type, potentially driving long-term balancing selection on loci within its epistatic network. Together, our results clarify both the biological relevance and the practical limitations of epistasis-aware analysis in human proteomic regulation.

Genomic sequencing has the potential to transform newborn screening (NBS) for rare diseases but raises significant pragmatic, clinical, psychosocial, ethical, and policy issues. Evidence is urgently needed to guide policy as healthcare systems around the world contemplate implementation. In 2025, four major genomic NBS (gNBS) studies, totaling over 10,800 newborns from the US, Belgium, and Australia, published initial results. The adoption of different approaches to key implementation issues in diverse healthcare systems by these studies allows us to draw comparisons and enable collective learning. All studies reported successful use of dried blood spots for DNA extraction, which supports integration with existing NBS infrastructure. Experience with automation of genomic data analysis and reporting was variable, with valuable insights gained about balancing sensitivity, specificity, scalability, and resource utilization going forward. The screen-positive rate ranged from 1.6% to 3.7%, with G6PD deficiency by far the most common condition identified. Further comparison of results was limited by wide variation in the number and type of conditions included and by inconsistencies in how outcomes were defined and reported, highlighting the need for greater harmonization of study designs and data collection. The ability to deliver gNBS at the scale and pace that would be required for a public screening program remains untested, and data on long-term outcomes and costs are still needed. Concerns also remain about inequitable access and outcomes, particularly for families at socioeconomic, linguistic, and geographical disadvantage, and these key questions need to be addressed next as the field continues to evolve.

Bone morphogenetic protein receptor type 2 (BMPR2) encodes an evolutionarily conserved serine/threonine kinase that phosphorylates type-1 BMP receptors to mediate intercellular communication upon ligand binding. Loss-of-function variants in BMPR2 are known to cause pulmonary arterial hypertension and other cardiovascular disorders. Here, we report a rare recurrent missense variant in BMPR2 (c.1126G>A [GenBank: NM_001204] [p.Glu376Lys]) identified in six individuals, who all present with neurodevelopmental phenotypes including autism spectrum disorder and global developmental delay. Trio analysis demonstrates de novo occurrence of this variant in at least five of the individuals. Using the fruit fly Drosophila melanogaster, we show that this variant behaves as a gain-of-function allele that acts in a ligand-independent but type-1 BMP receptor-dependent manner. BMPR2-specific inhibitors suppress excessive BMP activation induced by p.Glu376Lys variant expression in Drosophila, demonstrating its hypermorphic property. Finally, we show that this variant causes neurodevelopmental defects in flies when expressed in neurons or glial cells. Given that BMPR2 is expressed in various neural cell types in the human brain, ectopic activation of BMP signaling in multiple cell types is likely to contribute to the neurodevelopmental phenotypes observed in the probands.

Genome-wide association studies have identified genetic polymorphisms at 11p15 associated with systemic lupus erythematosus (lupus). Statistical fine mapping prioritizes a highly prevalent coding haplotype within IRF7. Analysis of ancient DNA confirms that this haplotype has persisted at high frequencies in the global population for millennia. The IRF7 risk haplotype is sufficient to increase nuclear localization of IRF7 and transcriptional activity downstream of pattern recognition receptor pathways. This risk haplotype increases IRF7 DNA-binding strength and alters IRF7 DNA sequence specificity, resulting in genotype-dependent increases in interferon-α production in numerous biological systems, including monocytes and airway epithelial cells. CRISPR engineering of the corresponding risk variant in mouse Irf7 results in both enhanced innate control of virus infection and increased autoantibody titers in a model of autoimmunity. Altogether, we establish a persistent and prominent IRF7 haplotype that amplifies IRF7 activity in a manner that has immunological risks and benefits.

Germline variants in cancer susceptibility genes (CSGs) are typically inherited rather than arising de novo. Hence, wide cascade testing of families across geographies is common, meaning consistency in variant classification is particularly critical. Variant interpretation requires collation of variant-level data from diverse sources, as well as assembly of comprehensive clinical data, often necessitating sharing of information between genomic testing centers. Here, we describe CanVar-UK, a freely accessible web platform bespoke designed to support interpretation of germline CSG variants. CanVar-UK contains variant-level data for over 1.1 million single-nucleotide variants (SNVs), comprising all possible coding SNVs in 116 established CSGs. The data sources with which variants are annotated include in silico scores from 11 clinically relevant tools, population allele frequencies from gnomAD v4.1, case counts from multiple cohorts, including National Health Service (NHS) clinical laboratory testing, variant-level readouts from 47 selected functional and splicing datasets across 19 CSGs, genetic epidemiology studies, and live linkage to existing consensus classifications in the ClinVar database. The diagnostic discussion forum is only available to registered diagnostic scientist users. Through this, a variant-tagged email message can be dispatched in real time across the diagnostic forum community of >1,500 users, with all exchanges and classifications captured and stored in the platform. Already widely used by NHS diagnostic clinical scientists in the UK, CanVar-UK has a rapidly growing international diagnostic user base (>800 UK and >600 non-UK registered users). Survey of the NHS diagnostic user community illustrates the wide-ranging utility of CanVar-UK within their clinical workflows for interpretation of germline CSG variants.

Hearing loss is a heterogeneous condition that can be classified into different subtypes with diverse genetic and cellular components. To investigate the cochlear cell types underlying the genetic basis of sensory and metabolic components of age-related hearing loss (ARHL), we integrated human genome-wide association study data with mouse cochlear single-cell RNA sequencing data using the single-cell disease relevance score tool. These analyses revealed that genes associated with the sensory component of ARHL were most highly expressed in hair cells, while genes associated with the metabolic component of ARHL were most highly expressed in spiral ganglion neurons. We also investigated whether ARHL-associated gene expression patterns differed across subpopulations of the same cell type. Sensory hearing loss-associated genes showed differential expression across supporting cell subpopulations in younger mice, whereas metabolic hearing loss-associated genes exhibited differences across intermediate cell subpopulations of the stria vascularis in older mice. These findings provide evidence for the role of distinct genetic and cellular risk profiles for different ARHL subtypes, suggesting that prevention and therapeutic strategies may require targeting specific cell populations at different life stages.

Genome-wide association studies identified a melanoma- and nevus count-associated locus on chromosome band 9q34.13. Fine-mapping and melanocyte expression data collectively suggest two potential risk genes with opposite associations with risk: higher levels of Rap guanine nucleotide exchange factor 1 (RAPGEF1) and lower levels of uridine-cytidine kinase 1 (UCK1). Colocalization analyses and conditional transcriptome-wide association studies (TWASs) suggest multiple causal cis-regulatory sequence variants in partial linkage disequilibrium (LD) to each other. Melanocyte capture-HiC and CRISPR inhibition demonstrated regulatory interactions between fine-mapped variants and the RAPGEF1 and UCK1 promoters. Focusing on RAPGEF1, we demonstrate that RAPGEF1 expression promotes melanocyte growth and drives colony formation of human immortalized melanocytes. Following treatment with human epidermal growth factor (EGF), RAPGEF1 overexpression activated both RAP1 and RAS. Further, we show that RAPGEF1 expression is significantly enriched in melanomas that lack strongly activating RAS-MAPK pathway mutations, which suggests that RAPGEF1 may promote oncogenic RAS-MAPK pathway signaling in melanomas. Furthermore, in these tumors, we provide preliminary evidence to support the prognostic relevance of RAPGEF1 expression in individuals whose melanomas lack RAS or BRAF mutations. Together with other recent studies, these data suggest that germline variation influencing RAS activation may play a key role in nevus development and melanoma risk.

ZNF536 encodes a C2H2 zinc-finger transcription factor that functions as a transcriptional repressor. While common noncoding variants at the ZNF536 locus have been reported to be associated with schizophrenia in a genome-wide association study (GWAS), the contribution of rare, protein-altering variants to human disease has not been systematically investigated. Through an international collaboration, we assembled a cohort of 21 affected individuals carrying 18 unique, rare, heterozygous, protein-altering ZNF536 variants. Most variants (15/18) were predicted loss-of-function (LoF) alleles, with the remainder being missense variants. Among families with available inheritance data (17/20), most variants arose de novo (12/17), while others were inherited from mosaic or mildly affected parents (5/17). Clinically, affected individuals presented with developmental delay along with high rates of autism spectrum disorder, intellectual disability, hyperactivity, aggressive behavior, anxiety, and hyperphagia; epilepsy and sleep disturbances were also frequently observed. To assess functional consequences of a proband-associated ZNF536 variant, we generated a Zfp536[p.Gln169Ter] knock-in mouse model. Homozygous mutants were non-viable, while heterozygotes survived but displayed autism-like behaviors, increased anxiety, and impaired recognition memory. Embryonic brain analysis revealed reduced cortical size, cortical thickness, and decreased deep-layer neuronal density. These features are consistent with phenotypes of a publicly available mouse knockout model and support our clinical cohort findings that rare monoallelic LoF variants in ZNF536 underlie a genetic neurodevelopmental disorder characterized by developmental delay, autism, and behavioral dysregulation. The pathogenicity of missense variants in disease remains to be determined. These results support a role for ZNF536 as a dosage-sensitive regulator of cortical development.