PROJECT SUMMARY/ABSTRACT Congenital hydrocephalus (CH) is the leading cause for brain surgery and is associated with marked neurodevelopmental disability. CH is traditionally considered a primary disorder of cerebrospinal fluid (CSF) homeostasis and thereby treated with surgical CSF shunting or endoscopic third ventriculostomy procedures to reduce CSF accumulation. One glaring concern is that ventriculomegaly often persists even after surgical intervention, and shunting does not consistently improve neurodevelopmental outcomes in many CH patients. While extensive research has identified new CH risk genes and highlighted their convergence in embryonic neuroepithelial stem cells, the causes of approximately 80% of CH cases remain unknown. This is partly due to genetic heterogeneity, reduced penetrance, and small sample sizes. Of note, non-European populations have been significantly underrepresented in existing genetic studies. Moreover, the impact of non-coding variants, structural variants, and somatic variants on CH mechanism remains largely uncharacterized. Additionally, the significant clinical variability observed among different subtypes of hydrocephalus has not been thoroughly evaluated at the molecular, cellular, and neuroimaging levels. Therefore, our objective is to establish a large and diverse cohort of primary CH patients, with a particular focus on non-European populations. Leveraging our expertise in genomics, neuroscience, neuroimaging, and pediatric neurology, we will enhance patient recruitment, generate and harmonize genomic and clinical data, and use WashU’s Central Neuroimaging Data Archive to automate quality control and image processing. This will create the largest CH cohort to date with whole-exome sequencing (WES; n = 2,879 [2,697 trios]) and whole-genome sequencing (WGS; n = 1,020 [648 trios]) data linked with comprehensive phenotypic and neuroimaging information to identify any remaining germline variants associated with CH. We will also perform integrative analyses of WES, WGS, transcriptomic data, and protein-protein interaction networks to uncover additional CH risk genes, pathways, and disease- associated cell types. To characterize somatic variants, we will conduct 500X WES on unaffected and affected brain tissues from approximately 100 patients and study their effects on gene expression and transcript splicing using bulk RNA-sequencing. Furthermore, to enhance diagnostic accuracy and establish a clinical and neuroimaging signature for CH, we will reevaluate neuroimaging, clinical, and genomic data and analyze genotype-phenotype correlations in patients with pathogenic or likely pathogenic (P/LP) variants in known and candidate genes associated with CH. To investigate factors influencing clinical variability, we will compare patients with CH and P/LP variants to controls without CH but with P/LP variants in the same genes. To facilitate data sharing, visualization, and analysis, we will establish the HYDRO-Seq Geno...