Detection of PatIent-Level distances from single cell genomics and pathomics data with Optimal Transport (PILOT) [article]

Mehdi Joodaki, Mina Shaigan, Victor Parra, Roman D. Buelow, Christoph Kuppe, David L. Holscher, Mingbo Cheng, James S. Nagai, Nassim Bouteldja, Vladimir Tesar, Jonathan Barratt, Ian S. D. Roberts (+4 others)
2022 bioRxiv   pre-print
Although clinical applications represent the next challenge in single-cell genomics and digital pathology, we are still lacking computational methods to analyse single-cell and pathomics data at a patient level for finding patient trajectories associated with diseases. This is challenging as a single-cell/pathomics data is represented by clusters of cells/structures, which cannot be easily compared with other samples. We here propose PatIent Level analysis with Optimal Transport (PILOT). PILOT
more » ... ses optimal transport to compute the Wasserstein distance between two single single-cell experiments. This allows us to perform unsupervised analysis at the sample level and to uncover trajectories associated with disease progression. Moreover, PILOT provides a statistical approach to delineate non-linear changes in cell populations, gene expression and tissues structures related to the disease trajectories. We evaluate PILOT and competing approaches in disease single-cell genomics and pathomics studies with up to 1.000 patients/donors and millions of cells or structures. Results demonstrate that PILOT detects disease-associated samples, cells, structures and genes from large and complex single-cell and pathomics data.
doi:10.1101/2022.12.16.520739 fatcat:yxtq6jvlkng73mraild675hq44