NeuroTri2-VISDOT: An open-access tool to harness the power of second trimester human single cell data to inform models of Mendelian neurodevelopmental disorders

Clark, K. J.; Lubin, E. E.; Gonzalez, E. M.; Sangree, A. K.; Layo-Carris, D. E.; Durham, E. L.; Ahrens-Nicklas, R. C.; Nomakuchi, T. T.; Bhoj, E. J. K.

doi:10.1101/2024.02.01.578438

bioRxiv · 10.1101/2024.02.01.578438

NeuroTri2-VISDOT: An open-access tool to harness the power of second trimester human single cell data to inform models of Mendelian neurodevelopmental disorders

Clark, K. J.·Lubin, E. E.·Gonzalez, E. M.·Sangree, A. K.·Layo-Carris, D. E.·Durham, E. L.·Ahrens-Nicklas, R. C.·Nomakuchi, T. T.·Bhoj, E. J. K.

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Abstract

Whole exome and genome sequencing, coupled with refined bioinformatic pipelines, have enabled improved diagnostic yields for individuals with Mendelian conditions and have led to the rapid identification of novel syndromes. For many Mendelian neurodevelopmental disorders (NDDs), there is a lack of pre-existing model systems for mechanistic work. Thus, it is critical for translational researchers to have an accessible phenotype- and genotype-informed approach for model system selection. Single-cell RNA sequencing data can be informative in such an approach, as it can indicate which cell types express a gene of interest at the highest levels across time. For Mendelian NDDs, such data for the developing human brain is especially useful. A valuable single-cell RNA sequencing dataset of the second trimester developing human brain was produced by Bhaduri et al in 2021, but access to these data can be limited by computing power and the learning curve of single-cell data analysis. To reduce these barriers for translational research on Mendelian NDDs, we have built the web-based tool, Neurodevelopment in Trimester 2 - VIsualization of Single cell Data Online Tool (NeuroTri2-VISDOT), for exploring this single-cell dataset, and we have employed it in several different settings to demonstrate its utility for the translational research community.

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Clark, K. J., Lubin, E. E., Gonzalez, E. M., Sangree, A. K., Layo-Carris, D. E., Durham, E. L., Ahrens-Nicklas, R. C., Nomakuchi, T. T., Bhoj, E. J. K.. 2024-02-04. NeuroTri2-VISDOT: An open-access tool to harness the power of second trimester human single cell data to inform models of Mendelian neurodevelopmental disorders. https://doi.org/10.1101/2024.02.01.578438

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