Abstract 2615: The Open Single-cell Pediatric Cancer Atlas project: Collaborative analysis of pediatric tumor data
Authors: Joshua A. Shapiro, Stephanie J. Spielman, Allegra G. Hawkins, Deepashree Venkatesh Prasad, Jennifer O'Malley, David S. Mejia, Jaclyn N. Taroni
Journal: Cancer Research (2025)

Abstract The Open Single-cell Pediatric Cancer Atlas (OpenScPCA) project is an open, collaborative project created to analyze publicly available data from the Single-cell Pediatric Cancer Atlas (ScPCA) Portal, with the goal of improving the quality and usability of single-cell pediatric cancer data and driving insights into pediatric cancer biology through deeper analysis of available data sets. The ScPCA Portal (https://scpca.alexslemonade.org/), developed and maintained by Alex’s Lemonade Stand Foundation (ALSF), is an open-source data resource for single-cell and single-nuclei RNA sequencing data of pediatric tumors. The ScPCA Portal currently contains summarized gene expression data for over 680 samples from a diverse set of over 50 types of cancers. All data on the portal is publicly available, uniformly processed with an open-source workflow, and ready for download in formats compatible with popular single-cell data analysis frameworks. To coordinate further analysis of the ScPCA data, we launched the OpenScPCA project in April 2024. The project aims to engage a broad community of researchers analyzing genomic data from pediatric tumors, building off the previous success of the Open Pediatric Brain Tumor Atlas project (Shapiro et al. 2023). As part of the OpenScPCA project, ALSF provides contributors with support through technical guidance, comprehensive documentation, and access to computational resources. We focused our initial collaborative efforts on the challenge of labeling cell types in pediatric cancer samples. Automated methods often have limited utility for annotating malignant cells in these samples because many tools and references for single-cell analysis were designed with adult healthy tissues or cancer types in mind. To overcome this limitation, we engage experts in various pediatric cancers who contribute their knowledge and analytical code. All contributions are publicly reviewed on GitHub for scientific content and code quality. In addition, we use automated testing to ensure that the annotation pipelines are robust and reusable. These combined efforts allow us to build a public resource to help improve pediatric cancer cell type annotation in this project and beyond. As we continue this ongoing work, we invite researchers with expertise in pediatric cancer gene expression and single-cell RNA-seq analysis to join the OpenScPCA Project. We hope those participating will discover new datasets to advance their research, gain experience with cutting-edge technologies, build their research portfolios, and join a supportive community. Get started at https://openscpca.readthedocs.io/en/latest/. Citation Format: Joshua A. Shapiro, Stephanie J. Spielman, Allegra G. Hawkins, Deepashree Venkatesh Prasad, Jennifer O'Malley, David S. Mejia, Jaclyn N. Taroni. The Open Single-cell Pediatric Cancer Atlas project: Collaborative analysis of pediatric tumor data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2615.