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Background Childhood glaucoma (CG) is a rare congenital eye disorder that causes a significant proportion of childhood blindness. Although the progress in genetic research and state-of-the-art technologies is ongoing, many glaucoma-associated genes are yet to be identified. Our study leveraged open access RNA-sequencing (RNA-seq) data of anterior segment tissues to identify novel genes and pathways potentially associated with the pathogenesis of CG, which can ultimately diagnose unsolved CG cases enrolled in the Genomics England 100,000 Genomes Project (GE100KGP).Methods The study used NCBI’s Gene Expression Omnibus (GEO) repository to retrieve a total of six RNA-seq datasets of anterior segment tissues. Genes were classified according to their expression patterns and potential role in cellular pathways associated with glaucoma. Candidate genes were investigated in our unsolved GE100KGP CG cohort and cross-checked in previously published glaucoma studies.Results Preliminary analysis identified genes like NTRK1 and PTPN7 with significantly different expression in trabecular meshwork, retinal ganglion cells, or human Tenon’s fibroblasts. These genes may regulate the dynamics of the extracellular matrix and intraocular pressure. Pathway enrichment analysis predicted MAPK signalling, TGF-beta signalling, and Wnt signalling to be enriched. A 1.04Mb deletion encompassing 12 genes and risk loci was identified in one CG subject and his affected mother. However, these results require further investigation to confirm their relevance to CG pathogenesis.Conclusions Despite the findings being inconclusive, this method highlights the utility of publicly available RNA-seq data as a useful resource for studying CG and directing future research on the molecular processes underlying the aetiology of the disease.