Publications

Despite advances in sequencing technologies and variant interpretation frameworks, many variants identified in genetic testing, particularly missense variants, remain classified as variants of uncertain significance (VUS), posing ongoing challenges in diagnosis and clinical management. This review explores the ongoing challenges of VUS interpretation in clinical genomics and its impact on patients, clinicians, and healthcare systems. We summarize established strategies that support VUS resolution, including large population reference databases, data-sharing initiatives, computational prediction tools, consensus-based guidelines, deep phenotyping, and functional validation assays. Building on these foundations, we highlight emerging approaches that leverage multi-omics analyses, high-throughput experimental platforms (e.g., saturation genome editing and cell-based morphological assays), and artificial intelligence-driven tools to improve scalability and interpretive accuracy. Together, these complementary approaches aim to reduce uncertainty, increase diagnostic yield, and enhance the clinical utility of genomic testing in both research and precision medicine.

Children with critical illness are vulnerable to nutritional deficits, which may contribute to increased susceptibility to infection, impaired immune function and delayed recovery. Optimizing nutritional support during acute illness is therefore essential to improving clinical outcomes. The complex interplay between critical illness, nutrition and infection is nuanced and requires careful consideration to minimize morbidity and mortality. In this narrative review, we synthesize current evidence and considerations regarding optimizing nutritional management to minimize infectious complications across neonatal and pediatric intensive care settings.

BACKGROUND: Haploinsufficiency of the RNA splicing regulator RBFOX2 has been linked to congenital heart disease, including hypoplastic left heart syndrome, yet its pathogenic mechanisms remain unresolved.

METHODS: Human induced pluripotent stem cells heterozygous or null for RBFOX2 were created and their cardiomyocyte (CM) derivatives were characterized in monolayer culture and engineered heart tissues. In addition to cellular phenotyping, molecular profiling by RNA sequencing and enhanced crosslinking and immunoprecipitation sequencing was performed to detect changes in gene expression, exon usage, and RBFOX2 (RNA-binding fox-1 homolog 2) binding. These data sets were integrated to identify RBFOX2-bound RNAs with altered expression and splicing and to compare them with publicly available data sets from progressive CM differentiation time points. Rescue experiments were performed in induced pluripotent stem cell-derived CMs, engineered heart tissues, and zebrafish.

RESULTS: We demonstrate that RBFOX2 is essential for CM differentiation by driving transcriptome maturation through gene expression- and alternative splicing-based isoform switching in transcripts primarily encoding sarcomere, cytoskeletal, and focal adhesion components, including the critical Z-disc factor ACTN2 (alpha-actinin-2). We further find that threshold levels of RBFOX2 facilitate autoregulatory splicing of mutually exclusive exons, generating early and late RBFOX2 isoforms with distinct functions. In heterozygous CMs, this threshold is not reached, resulting in isoform imbalance and production of an aberrant transcript, which further reduces functional RBFOX2 levels to well below 50% of wild-type. Finally, we demonstrate that ACTN2 overexpression rescues heterozygous, but not null, phenotypes, suggesting that ACTN2 activates an RBFOX2-dependent feedback loop that promotes transcriptome maturation.

CONCLUSIONS: Our data demonstrate that reduced RBFOX2 dosage and impaired autoregulation stall CM differentiation by inhibiting transcriptome maturation, contributing to congenital heart disease pathogenesis and potentially increasing heart failure susceptibility following surgical intervention.

Folate deficiency is associated with increased risk of conotruncal heart defects (CTHD), but its interaction with genetic factors remains unclear. Our objective was to investigate genome-wide associations between common genetic variants and birth before versus after universal folic acid fortification among children with CTHD and other heart defects. Sequencing data were available through the Pediatric Cardiac Genomics Consortium, aligned to the human reference genome (GRCh38/hg38), and jointly processed to ensure uniform variant detection and minimize batch effects. Analyses were restricted to individuals with European-inferred genetic ancestry, limiting generalizability to other ancestral groups. Genome-wide association study (GWAS) models compared allele frequencies across fortification eras among all participants (n = 1285), the subset with CTHD (n = 534), and the remaining individuals with other heart defects (n = 751). Functional enrichment was assessed using the Database for Annotation, Visualization and Integrated Discovery (DAVID). Among the full analytic group, eight loci had at least two suggestive variants before compared to after fortification. Among the subset with CTHD, two variants located in DHRS3 (rs7551703, odds ratio [OR] 2.10, and rs6541043, OR 2.21) and four variants located in PPARGC1B showed suggestive association after fortification (OR 4.47-4.51). Enriched biological pathway terms were consistent with cardiac developmental processes. In summary, this study examined the association between folic acid fortification and genetic risk for CTHD and other heart defects and identified associations with fortification era that suggest some shift in risk following fortification. Identified pathways suggest gene-nutrient interactions may modulate cardiac developmental pathways, underscoring the relationship between maternal folate status and cardiovascular development.

OBJECTIVE: To determine the incremental risks of mortality and major neonatal morbidities associated with congenital heart disease (CHD) beyond prematurity alone.

STUDY DESIGN: Secondary analysis of two North American neonatal registries (2010-2022) including infants <35 weeks' gestation: 11,221 with CHD from the Children's Hospitals Neonatal Consortium and 720,846 without CHD from the Vermont Oxford Network. The primary outcome was in-hospital mortality. Secondary outcomes were major neonatal morbidities.

RESULTS: Preterm infants with CHD had fourfold higher odds of in-hospital mortality (OR 4.0, 95% CI 3.76-4.21). Mortality was similar at ≤26 weeks' gestation, but the relative impact of CHD increased with advancing gestational age. CHD was associated with significantly increased risks of severe bronchopulmonary dysplasia, intraventricular hemorrhage, and necrotizing enterocolitis.

CONCLUSION: The impact of CHD on mortality is gestational age dependent, with prematurity predominating at the lowest gestational ages and CHD increasingly driving mortality as gestational maturity improves.

The first 1,000 days of brain development are sensitive to nutrient availability, and large longitudinal early-life cohorts provide an opportunity to study early nutritional influences on neurodevelopment in generally healthy populations. We aimed to identify international pregnancy and birth cohorts with at least 1,000 children collecting early-life nutrition data, including maternal nutrition during pregnancy or lactation, breastfeeding, and solid-food feeding, along with later child neurodevelopmental outcomes. In total, 104 pregnancy and birth cohorts were identified, representing over 1.17 million children across 41 countries. Cohorts spanned six continents, with the largest participant representation from high- and upper middle-income settings. Maternal diet during pregnancy and breastfeeding status were the most frequently captured nutrition domains, while neurodevelopmental assessments varied across developmental periods, using over 200 assessment tools. These cohorts support future harmonized analyses of early nutrition and neurodevelopment, and further work will benefit from international collaboration, shared data standards, and pooled or federated infrastructures.

With dramatic advancements in biological data generation, genetic rescue and reproductive technologies, and inter-institutional coordination of care across entire animal populations, zoos, aquariums, and their collaborators are uniquely positioned to lead population-wide research benefiting animal wellbeing and species survival. However, procedural and inter-institutional barriers make it exceedingly difficult to access existing zoological biospecimens and data at scale. To address this, the Zoonomics Working Group, representing diverse roles across three zoological associations (AZA, EAZA, WAZA), proposes a biodiversity biobank alliance that develops and delivers shared resources to support the collection, storage, and sharing of biological samples and associated data across the zoological and conservation community. By biobank alliance, we mean a community-guided effort that develops shared resources, standards, ethos, and practices for collecting, storing, and sharing biological samples and associated data voluntarily through transparent processes, consistent with professional accreditation standards and international best practices. While initially focused on addressing the needs and regulatory landscape of U.S. institutions, the alliance is designed to create frameworks that are adaptable and adoptable for international expansion. Such a framework would help the zoological community navigate the ethical, legal, and practical challenges of managing biospecimen collections, making access more efficient, reliable, and robust. Achieving this vision requires collective agreement on ethical principles such as reciprocity, transparency, and data stewardship, ensuring that research is both feasible and proactively supported. Such coordination will drive advances in fundamental biology and accelerate progress in animal health, welfare, management, and biodiversity conservation.

BACKGROUND: Congenital heart disease (CHD) is the most common major congenital anomaly and a leading cause of infant morbidity and mortality. The rapid expansion of genomic technologies has accelerated the discovery of rare genetic variants implicated in CHD pathogenesis. However, most individuals with CHD still lack an identifiable molecular etiology. The purpose of this scoping review is to systematically characterize genes reported in the recent literature as candidate CHD-associated genes and contextualize these findings within the stages of cardiac morphogenesis.

METHODS: PubMed was searched using predefined terms related to CHD and genetic variants, supplemented by a prospectively maintained internal database. We included human studies published between January 2023 and December 2025 that identified pathogenic, likely pathogenic, or uncertain monogenic variants in at least one patient with CHD. Animal-only studies, chromosomal abnormalities, copy number variants, multigenic associations, transcriptomic/proteomic analyses, reviews, and maternal-only genetic studies were excluded. Gene-disease validity classifications were assigned using the Clinical Genome Resource (ClinGen) CHD Gene Curation Expert Panel framework.

RESULTS: Of 2,834 screened articles, 391 studies met inclusion criteria, identifying 912 unique genes reported as candidate CHD-associated genes. Frequently reported genes included PTPN11, NOTCH1, GATA4, JAG1, MYH6, GATA6, and LZTR1. Identified genes spanned all major stages of cardiogenesis, including developmental priming, cardiac progenitor specification, left-right axis formation, neural crest migration, outflow tract development, septation, and postnatal structural remodeling. Studies increasingly implicated ciliary dysfunction, transcriptional regulation, ribosomal biology, and multigenic inheritance in CHD pathogenesis. Emerging methodologies included stem cell-derived cardiac models, machine learning-based gene prioritization, and epigenetic analyses.

CONCLUSIONS: Recent literature substantially expands the catalog of candidate genes that may be associated with CHD and highlights the biologic complexity underlying cardiac morphogenesis. Integration of genomic, developmental, and functional approaches will be essential to improve mechanistic understanding, refine genetic counseling, and support future precision medicine strategies for CHD.

Neurodevelopmental disorders encompass a large group of conditions, many of which can be explained by genetic variants. KIRREL3 has previously been associated with neurodevelopmental disorders and is expressed in the developing human basal ganglia and amygdala. Through GeneMatcher, which allows clinicians, families, and researchers to share information about novel gene variants, and the Simons Foundation Powering Autism Research (SPARK) project, we identified 26 individuals with different rare missense variants in KIRREL3, which were predicted to be damaging based on their REVEL score. All probands had neurodevelopmental diagnoses including autism spectrum disorder, global developmental delay, intellectual disability, or a learning disability. A full review of previous publications identified 10 rare KIRREL3 missense variants in 13 individuals who had at least one diagnosis of an autism spectrum disorder or intellectual disability. These findings highlight the potential role of KIRREL3 missense variants in neurodevelopmental disorders, which warrants further study.